[med-svn] [Git][med-team/snakemake][debian_for_upstream_5.14.0_which_requires_conda] 3 commits: Use https for links where available.
Rebecca N. Palmer
gitlab at salsa.debian.org
Fri Apr 24 18:54:56 BST 2020
Rebecca N. Palmer pushed to branch debian_for_upstream_5.14.0_which_requires_conda at Debian Med / snakemake
Commits:
148f0055 by Rebecca N. Palmer at 2020-04-24T16:42:38+01:00
Use https for links where available.
- - - - -
fa393738 by Rebecca N. Palmer at 2020-04-24T16:44:27+01:00
Fix rather than disable broken test_cluster_sync
- - - - -
7d50f8d3 by Rebecca N. Palmer at 2020-04-24T17:07:11+01:00
edit patch descriptions, include upstream status
- - - - -
8 changed files:
- debian/changelog
- debian/patches/0009-skip-test-without-google-cloud-sdk.patch
- + debian/patches/bug322_cluster_sync.patch
- + debian/patches/link_security.patch
- debian/patches/series
- debian/patches/workaround_sphinx_issue.patch
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -10,7 +10,8 @@ snakemake (5.14.0-1) UNRELEASED; urgency=medium
[ Rebecca N. Palmer ]
* Use Python 3 in subprocess calls.
- * Disable buggy test (upstream 322) and tests needing conda or docker.
+ * Fix buggy test (upstream 322).
+ * Disable tests needing conda or docker.
* Delete unused patches.
* Use boto3 (like upstream) not boto.
* Reproducibility: don't ship (timestamped) test logs.
@@ -20,6 +21,7 @@ snakemake (5.14.0-1) UNRELEASED; urgency=medium
* Update dependencies, add minimal-Depends test.
* Privacy: use local dagre-d3, add missing Javascript dependencies,
don't appear to show live status when we don't.
+ * Use https for links where available.
-- Rebecca N. Palmer <rebecca_palmer at zoho.com> Thu, 09 Apr 2020 14:57:00 +0100
=====================================
debian/patches/0009-skip-test-without-google-cloud-sdk.patch
=====================================
@@ -1,14 +1,10 @@
-From: chrysn <chrysn at fsfe.org>
-Date: Mon, 11 Dec 2017 16:15:05 +0100
-Subject: Skip tests with that depend on google-cloud-sdk if not installed
-Forwarded: no
+Description: Skip tests that depend on google-cloud-sdk if not installed
-There is no package in Debian that provides the required module, and its
-absence makes the test fail.
+This is not currently in Debian - see RFP #759578.
+
+Author: chrysn <chrysn at fsfe.org>
+Forwarded: not-needed
-Whether this needs a Debian RFP or should be forwarded is undecided yet given
-the author has no clue about what those Google Cloud SDK actually does.
----
--- a/tests/test_remote_gs/Snakefile
+++ b/tests/test_remote_gs/Snakefile
@@ -1,15 +1,19 @@
=====================================
debian/patches/bug322_cluster_sync.patch
=====================================
@@ -0,0 +1,16 @@
+Description: Allow running tests in parallel
+
+Author: Rebecca N. Palmer <rebecca_palmer at zoho.com>
+Bug: https://github.com/snakemake/snakemake/issues/322
+Forwarded: accepted https://github.com/snakemake/snakemake/pull/326
+
+--- a/tests/tests.py
++++ b/tests/tests.py
+@@ -244,6 +244,7 @@ def test_remote():
+
+
+ def test_cluster_sync():
++ os.environ["TESTVAR"] = "test"
+ run(dpath("test14"), snakefile="Snakefile.nonstandard", cluster_sync="./qsub")
+
+
=====================================
debian/patches/link_security.patch
=====================================
@@ -0,0 +1,683 @@
+Description: Change links to HTTPS where available
+
+Author: Rebecca N. Palmer <rebecca_palmer at zoho.com>
+Forwarded: accepted https://github.com/snakemake/snakemake/pull/325
+
+diff --git a/docs/executing/cluster-cloud.rst b/docs/executing/cluster-cloud.rst
+index 9bb1a8b3..988ad2fe 100644
+--- a/docs/executing/cluster-cloud.rst
++++ b/docs/executing/cluster-cloud.rst
+@@ -236,7 +236,7 @@ and forward it to the cluster scheduler:
+
+ $ snakemake --cluster "qsub --runtime {params.runtime}"
+
+-If your cluster system supports `DRMAA <http://www.drmaa.org/>`_, Snakemake can make use of that to increase the control over jobs.
++If your cluster system supports `DRMAA <https://www.drmaa.org/>`_, Snakemake can make use of that to increase the control over jobs.
+ E.g. jobs can be cancelled upon pressing ``Ctrl+C``, which is not possible with the generic ``--cluster`` support.
+ With DRMAA, no ``qsub`` command needs to be provided, but system specific arguments can still be given as a string, e.g.
+
+diff --git a/docs/executing/interoperability.rst b/docs/executing/interoperability.rst
+index d33d3b75..a8fc26ee 100644
+--- a/docs/executing/interoperability.rst
++++ b/docs/executing/interoperability.rst
+@@ -9,7 +9,7 @@ Interoperability
+ CWL export
+ ----------
+
+-Snakemake workflows can be exported to `CWL <http://www.commonwl.org/>`_, such that they can be executed in any `CWL-enabled workflow engine <https://www.commonwl.org/#Implementations>`_.
++Snakemake workflows can be exported to `CWL <https://www.commonwl.org/>`_, such that they can be executed in any `CWL-enabled workflow engine <https://www.commonwl.org/#Implementations>`_.
+ Since, CWL is less powerful for expressing workflows than Snakemake (most importantly Snakemake offers more flexible scatter-gather patterns, since full Python can be used), export works such that every Snakemake job is encoded into a single step in the CWL workflow.
+ Moreover, every step of that workflow calls Snakemake again to execute the job. The latter enables advanced Snakemake features like scripts, benchmarks and remote files to work inside CWL.
+ So, when exporting keep in mind that the resulting CWL file can become huge, depending on the number of jobs in your workflow.
+diff --git a/docs/index.rst b/docs/index.rst
+index 164f6a3e..a448f1f0 100644
+--- a/docs/index.rst
++++ b/docs/index.rst
+@@ -113,7 +113,7 @@ Support
+ Citation
+ --------
+
+-`Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012. <http://bioinformatics.oxfordjournals.org/content/28/19/2520>`_
++`Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012. <https://bioinformatics.oxfordjournals.org/content/28/19/2520>`_
+
+ See :doc:`Citations <project_info/citations>` for more information.
+
+@@ -154,41 +154,41 @@ Please consider to add your own.
+ * Goormaghtigh et al. 2018. `Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells <https://mbio.asm.org/content/mbio/9/3/e00640-18.full.pdf>`_. mBio.
+ * Ramirez et al. 2018. `Detecting macroecological patterns in bacterial communities across independent studies of global soils <https://www.nature.com/articles/s41564-017-0062-x>`_. Nature microbiology.
+ * Amato et al. 2018. `Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes <https://www.nature.com/articles/s41396-018-0175-0>`_. The ISME journal.
+-* Uhlitz et al. 2017. `An immediate–late gene expression module decodes ERK signal duration <http://msb.embopress.org/content/13/5/928>`_. Molecular Systems Biology.
+-* Akkouche et al. 2017. `Piwi Is Required during Drosophila Embryogenesis to License Dual-Strand piRNA Clusters for Transposon Repression in Adult Ovaries <http://www.sciencedirect.com/science/article/pii/S1097276517302071>`_. Molecular Cell.
++* Uhlitz et al. 2017. `An immediate–late gene expression module decodes ERK signal duration <https://msb.embopress.org/content/13/5/928>`_. Molecular Systems Biology.
++* Akkouche et al. 2017. `Piwi Is Required during Drosophila Embryogenesis to License Dual-Strand piRNA Clusters for Transposon Repression in Adult Ovaries <https://www.sciencedirect.com/science/article/pii/S1097276517302071>`_. Molecular Cell.
+ * Beatty et al. 2017. `Giardia duodenalis induces pathogenic dysbiosis of human intestinal microbiota biofilms <https://www.ncbi.nlm.nih.gov/pubmed/28237889>`_. International Journal for Parasitology.
+ * Meyer et al. 2017. `Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400397/>`_. Molecular Biology and Evolution.
+-* Lonardo et al. 2017. `Priming of soil organic matter: Chemical structure of added compounds is more important than the energy content <http://www.sciencedirect.com/science/article/pii/S0038071716304539>`_. Soil Biology and Biochemistry.
++* Lonardo et al. 2017. `Priming of soil organic matter: Chemical structure of added compounds is more important than the energy content <https://www.sciencedirect.com/science/article/pii/S0038071716304539>`_. Soil Biology and Biochemistry.
+ * Beisser et al. 2017. `Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes <https://peerj.com/articles/2832/>`_. PeerJ.
+ * Piro et al 2017. `MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling <https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0318-y>`_. Microbiome.
+ * Dimitrov et al 2017. `Successive DNA extractions improve characterization of soil microbial communities <https://peerj.com/articles/2915/>`_. PeerJ.
+-* de Bourcy et al. 2016. `Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging <http://www.pnas.org/content/114/5/1105.short>`_. PNAS.
+-* Bray et al. 2016. `Near-optimal probabilistic RNA-seq quantification <http://www.nature.com/nbt/journal/v34/n5/abs/nbt.3519.html>`_. Nature Biotechnology.
++* de Bourcy et al. 2016. `Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging <https://www.pnas.org/content/114/5/1105.short>`_. PNAS.
++* Bray et al. 2016. `Near-optimal probabilistic RNA-seq quantification <https://www.nature.com/nbt/journal/v34/n5/abs/nbt.3519.html>`_. Nature Biotechnology.
+ * Etournay et al. 2016. `TissueMiner: a multiscale analysis toolkit to quantify how cellular processes create tissue dynamics <https://elifesciences.org/content/5/e14334>`_. eLife Sciences.
+-* Townsend et al. 2016. `The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice <http://www.cell.com/cancer-cell/abstract/S1535-6108%2816%2930090-3>`_. Cancer Cell.
+-* Burrows et al. 2016. `Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs <http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005793>`_. PLOS Genetics.
+-* Ziller et al. 2015. `Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing <http://www.nature.com/nmeth/journal/v12/n3/full/nmeth.3152.html>`_. Nature Methods.
++* Townsend et al. 2016. `The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice <https://www.cell.com/cancer-cell/abstract/S1535-6108%2816%2930090-3>`_. Cancer Cell.
++* Burrows et al. 2016. `Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs <https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005793>`_. PLOS Genetics.
++* Ziller et al. 2015. `Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing <https://www.nature.com/nmeth/journal/v12/n3/full/nmeth.3152.html>`_. Nature Methods.
+ * Li et al. 2015. `Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0843-6>`_. Genome Biology.
+-* Schmied et al. 2015. `An automated workflow for parallel processing of large multiview SPIM recordings <http://bioinformatics.oxfordjournals.org/content/32/7/1112>`_. Bioinformatics.
+-* Chung et al. 2015. `Whole-Genome Sequencing and Integrative Genomic Analysis Approach on Two 22q11.2 Deletion Syndrome Family Trios for Genotype to Phenotype Correlations <http://onlinelibrary.wiley.com/doi/10.1002/humu.22814/full>`_. Human Mutation.
+-* Kim et al. 2015. `TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms <http://emboj.embopress.org/content/34/13/1801.long>`_. The EMBO Journal.
+-* Park et al. 2015. `Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone <http://doi.org/10.1016/j.cell.2015.06.007>`_. Cell.
+-* Břinda et al. 2015. `RNF: a general framework to evaluate NGS read mappers <http://bioinformatics.oxfordjournals.org/content/early/2015/09/30/bioinformatics.btv524>`_. Bioinformatics.
+-* Břinda et al. 2015. `Spaced seeds improve k-mer-based metagenomic classification <http://bioinformatics.oxfordjournals.org/content/early/2015/08/10/bioinformatics.btv419>`_. Bioinformatics.
++* Schmied et al. 2015. `An automated workflow for parallel processing of large multiview SPIM recordings <https://bioinformatics.oxfordjournals.org/content/32/7/1112>`_. Bioinformatics.
++* Chung et al. 2015. `Whole-Genome Sequencing and Integrative Genomic Analysis Approach on Two 22q11.2 Deletion Syndrome Family Trios for Genotype to Phenotype Correlations <https://onlinelibrary.wiley.com/doi/10.1002/humu.22814/full>`_. Human Mutation.
++* Kim et al. 2015. `TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms <https://emboj.embopress.org/content/34/13/1801.long>`_. The EMBO Journal.
++* Park et al. 2015. `Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone <https://doi.org/10.1016/j.cell.2015.06.007>`_. Cell.
++* Břinda et al. 2015. `RNF: a general framework to evaluate NGS read mappers <https://bioinformatics.oxfordjournals.org/content/early/2015/09/30/bioinformatics.btv524>`_. Bioinformatics.
++* Břinda et al. 2015. `Spaced seeds improve k-mer-based metagenomic classification <https://bioinformatics.oxfordjournals.org/content/early/2015/08/10/bioinformatics.btv419>`_. Bioinformatics.
+ * Spjuth et al. 2015. `Experiences with workflows for automating data-intensive bioinformatics <https://biologydirect.biomedcentral.com/articles/10.1186/s13062-015-0071-8>`_. Biology Direct.
+-* Schramm et al. 2015. `Mutational dynamics between primary and relapse neuroblastomas <http://www.nature.com/ng/journal/v47/n8/full/ng.3349.html>`_. Nature Genetics.
+-* Berulava et al. 2015. `N6-Adenosine Methylation in MiRNAs <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118438>`_. PLOS ONE.
+-* The Genome of the Netherlands Consortium 2014. `Whole-genome sequence variation, population structure and demographic history of the Dutch population <http://www.nature.com/ng/journal/v46/n8/full/ng.3021.html>`_. Nature Genetics.
+-* Patterson et al. 2014. `WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads <http://online.liebertpub.com/doi/10.1089/cmb.2014.0157>`_. Journal of Computational Biology.
+-* Fernández et al. 2014. `H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells <http://genome.cshlp.org/content/25/1/27.long>`_. Genome Research.
++* Schramm et al. 2015. `Mutational dynamics between primary and relapse neuroblastomas <https://www.nature.com/ng/journal/v47/n8/full/ng.3349.html>`_. Nature Genetics.
++* Berulava et al. 2015. `N6-Adenosine Methylation in MiRNAs <https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118438>`_. PLOS ONE.
++* The Genome of the Netherlands Consortium 2014. `Whole-genome sequence variation, population structure and demographic history of the Dutch population <https://www.nature.com/ng/journal/v46/n8/full/ng.3021.html>`_. Nature Genetics.
++* Patterson et al. 2014. `WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads <https://online.liebertpub.com/doi/10.1089/cmb.2014.0157>`_. Journal of Computational Biology.
++* Fernández et al. 2014. `H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells <https://genome.cshlp.org/content/25/1/27.long>`_. Genome Research.
+ * Köster et al. 2014. `Massively parallel read mapping on GPUs with the q-group index and PEANUT <https://peerj.com/articles/606/>`_. PeerJ..
+-* Chang et al. 2014. `TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications <http://www.cell.com/molecular-cell/abstract/S1097-2765(14)00121-X>`_. Molecular Cell.
+-* Althoff et al. 2013. `MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A <http://onlinelibrary.wiley.com/doi/10.1002/ijc.28091/abstract;jsessionid=33613A834E2A2FDCCA49246C23DF777E.f04t02>`_. International Journal of Cancer.
+-* Marschall et al. 2013. `MATE-CLEVER: Mendelian-Inheritance-Aware Discovery and Genotyping of Midsize and Long Indels <http://bioinformatics.oxfordjournals.org/content/29/24/3143.long>`_. Bioinformatics.
+-* Rahmann et al. 2013. `Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data <http://www.sciencedirect.com/science/article/pii/S1046202312002605>`_. Methods.
+-* Martin et al. 2013. `Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3 <http://www.nature.com/ng/journal/v45/n8/full/ng.2674.html>`_. Nature Genetics.
+-* Czeschik et al. 2013. `Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome <http://link.springer.com/article/10.1007%2Fs00439-013-1295-2>`_. Human Genetics.
+-* Marschall et al. 2012. `CLEVER: Clique-Enumerating Variant Finder <http://bioinformatics.oxfordjournals.org/content/28/22/2875.long>`_. Bioinformatics.
++* Chang et al. 2014. `TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications <https://www.cell.com/molecular-cell/abstract/S1097-2765(14)00121-X>`_. Molecular Cell.
++* Althoff et al. 2013. `MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A <https://onlinelibrary.wiley.com/doi/10.1002/ijc.28091/abstract;jsessionid=33613A834E2A2FDCCA49246C23DF777E.f04t02>`_. International Journal of Cancer.
++* Marschall et al. 2013. `MATE-CLEVER: Mendelian-Inheritance-Aware Discovery and Genotyping of Midsize and Long Indels <https://bioinformatics.oxfordjournals.org/content/29/24/3143.long>`_. Bioinformatics.
++* Rahmann et al. 2013. `Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data <https://www.sciencedirect.com/science/article/pii/S1046202312002605>`_. Methods.
++* Martin et al. 2013. `Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3 <https://www.nature.com/ng/journal/v45/n8/full/ng.2674.html>`_. Nature Genetics.
++* Czeschik et al. 2013. `Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome <https://link.springer.com/article/10.1007%2Fs00439-013-1295-2>`_. Human Genetics.
++* Marschall et al. 2012. `CLEVER: Clique-Enumerating Variant Finder <https://bioinformatics.oxfordjournals.org/content/28/22/2875.long>`_. Bioinformatics.
+
+
+ .. toctree::
+diff --git a/docs/project_info/citations.rst b/docs/project_info/citations.rst
+index a21b7344..07d2f5a4 100644
+--- a/docs/project_info/citations.rst
++++ b/docs/project_info/citations.rst
+@@ -18,7 +18,7 @@ When using Snakemake for a publication, **please cite the following article** in
+ Cite This
+ =========
+
+-`Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012. <http://bioinformatics.oxfordjournals.org/content/28/19/2520>`_
++`Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012. <https://bioinformatics.oxfordjournals.org/content/28/19/2520>`_
+
+
+ More References
+@@ -26,11 +26,11 @@ More References
+
+ Another publication describing more of Snakemake internals:
+
+-`Köster, Johannes and Rahmann, Sven. "Building and Documenting Bioinformatics Workflows with Python-based Snakemake". Proceedings of the GCB 2012. <http://drops.dagstuhl.de/opus/volltexte/oasics-complete/oasics-vol26-gcb2012-complete.pdf>`_
++`Köster, Johannes and Rahmann, Sven. "Building and Documenting Bioinformatics Workflows with Python-based Snakemake". Proceedings of the GCB 2012. <https://drops.dagstuhl.de/opus/volltexte/oasics-complete/oasics-vol26-gcb2012-complete.pdf>`_
+
+ And my PhD thesis which describes all algorithmic details:
+
+-`Johannes Köster, "Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis", TU Dortmund 2014 <http://hdl.handle.net/2003/33940>`_
++`Johannes Köster, "Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis", TU Dortmund 2014 <https://hdl.handle.net/2003/33940>`_
+
+
+ Project Pages
+@@ -48,4 +48,4 @@ The markdown syntax is
+ [](https://snakemake.readthedocs.io)
+
+ Replace the ``3.5.2`` with the minimum required Snakemake version.
+-You can also `change the style <http://shields.io/#styles>`_.
++You can also `change the style <https://shields.io/#styles>`_.
+diff --git a/docs/project_info/faq.rst b/docs/project_info/faq.rst
+index e1ef4d2a..d80010d9 100644
+--- a/docs/project_info/faq.rst
++++ b/docs/project_info/faq.rst
+@@ -188,7 +188,7 @@ and have in the Snakefile some Python code that reads this environment variable,
+ I get a NameError with my shell command. Are braces unsupported?
+ ----------------------------------------------------------------
+
+-You can use the entire Python `format minilanguage <http://docs.python.org/3/library/string.html#formatspec>`_ in shell commands. Braces in shell commands that are not intended to insert variable values thus have to be escaped by doubling them:
++You can use the entire Python `format minilanguage <https://docs.python.org/3/library/string.html#formatspec>`_ in shell commands. Braces in shell commands that are not intended to insert variable values thus have to be escaped by doubling them:
+
+ This:
+
+@@ -315,7 +315,7 @@ On unix, you can make use of the commonly pre-installed `mail` command:
+ snakemake 2> snakemake.log
+ mail -s "snakemake finished" youremail at provider.com < snakemake.log
+
+-In case your administrator does not provide you with a proper configuration of the sendmail framework, you can configure `mail` to work e.g. via Gmail (see `here <http://www.cyberciti.biz/tips/linux-use-gmail-as-a-smarthost.html>`_).
++In case your administrator does not provide you with a proper configuration of the sendmail framework, you can configure `mail` to work e.g. via Gmail (see `here <https://www.cyberciti.biz/tips/linux-use-gmail-as-a-smarthost.html>`_).
+
+ I want to pass variables between rules. Is that possible?
+ ---------------------------------------------------------
+diff --git a/docs/project_info/more_resources.rst b/docs/project_info/more_resources.rst
+index b62d1fa1..dd0783ec 100644
+--- a/docs/project_info/more_resources.rst
++++ b/docs/project_info/more_resources.rst
+@@ -14,8 +14,8 @@ Talks and Posters
+ * `Invited talk by Johannes Köster at the Broad Institute, Boston 2015. <https://slides.com/johanneskoester/snakemake-broad-2015>`_
+ * `Introduction to Snakemake. Tutorial Slides presented by Johannes Köster at the GCB 2015, Dortmund, Germany. <https://slides.com/johanneskoester/deck-1>`_
+ * `Invited talk by Johannes Köster at the DTL Focus Meeting: "NGS Production Pipelines", Dutch Techcentre for Life Sciences, Utrecht 2014. <https://speakerdeck.com/johanneskoester/workflow-management-with-snakemake>`_
+-* `Taming Snakemake by Jeremy Leipzig, Bioinformatics software developer at Children's Hospital of Philadelphia, 2014. <http://de.slideshare.net/jermdemo/taming-snakemake>`_
+-* `"Snakemake makes ... snakes?" - An Introduction by Marcel Martin from SciLifeLab, Stockholm 2015 <http://marcelm.net/talks/2015/snakemake>`_
++* `Taming Snakemake by Jeremy Leipzig, Bioinformatics software developer at Children's Hospital of Philadelphia, 2014. <https://de.slideshare.net/jermdemo/taming-snakemake>`_
++* `"Snakemake makes ... snakes?" - An Introduction by Marcel Martin from SciLifeLab, Stockholm 2015 <https://marcelm.net/talks/2015/snakemake>`_
+ * `"Workflow Management with Snakemake" by Johannes Köster, 2015. Held at the Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute <https://speakerdeck.com/johanneskoester/workflow-management-with-snakemake-1>`_
+
+
+@@ -27,14 +27,14 @@ External Resources
+
+ These resources are not part of the official documentation.
+
+-* `A number of tutorials on the subject "Tools for reproducible research" <http://nbis-reproducible-research.readthedocs.io>`_
++* `A number of tutorials on the subject "Tools for reproducible research" <https://nbis-reproducible-research.readthedocs.io>`_
+ * `Snakemake workflow used for the Kallisto paper <https://github.com/pachterlab/kallisto_paper_analysis>`_
+-* `An alternative tutorial for Snakemake <http://slowkow.com/notes/snakemake-tutorial/>`_
++* `An alternative tutorial for Snakemake <https://slowkow.com/notes/snakemake-tutorial/>`_
+ * `An Emacs mode for Snakemake <http://melpa.milkbox.net/#/snakemake-mode>`_
+ * `Flexible bioinformatics pipelines with Snakemake <http://watson.nci.nih.gov/~sdavis/blog/flexible_bioinformatics_pipelines_with_snakemake/>`_
+ * `Sandwiches with Snakemake <https://github.com/leipzig/SandwichesWithSnakemake>`_
+-* `A visualization of the past years of Snakemake development <http://youtu.be/bq3vXrWw1yk>`_
++* `A visualization of the past years of Snakemake development <https://youtu.be/bq3vXrWw1yk>`_
+ * `Japanese version of the Snakemake tutorial <https://github.com/joemphilips/Translate_Snakemake_Tutorial>`_
+-* `Basic <http://bioinfo-fr.net/snakemake-pour-les-nuls>`_ and `advanced <http://bioinfo-fr.net/snakemake-aller-plus-loin-avec-la-parallelisation>`_ french Snakemake tutorial.
++* `Basic <https://bioinfo-fr.net/snakemake-pour-les-nuls>`_ and `advanced <https://bioinfo-fr.net/snakemake-aller-plus-loin-avec-la-parallelisation>`_ french Snakemake tutorial.
+ * `Mini tutorial on Snakemake and Bioconda <https://github.com/dlaehnemann/TutMinicondaSnakemake>`_
+ * `Snakeparse: a utility to expose Snakemake workflow configuation via a command line interface <https://github.com/nh13/snakeparse>`_
+diff --git a/docs/snakefiles/configuration.rst b/docs/snakefiles/configuration.rst
+index 403e6ff7..e4037b8f 100644
+--- a/docs/snakefiles/configuration.rst
++++ b/docs/snakefiles/configuration.rst
+@@ -64,7 +64,7 @@ With the `Pandas library <https://pandas.pydata.org/>`_ such data can be read an
+ samples = pd.read_table("samples.tsv").set_index("samples", drop=False)
+
+ reads in a table ``samples.tsv`` in TSV format and makes every record accessible by the sample name.
+-For details, see the `Pandas documentation <http://pandas.pydata.org/pandas-docs/stable/generated/pandas.read_table.html?highlight=read_table#pandas-read-table>`_.
++For details, see the `Pandas documentation <https://pandas.pydata.org/pandas-docs/stable/generated/pandas.read_table.html?highlight=read_table#pandas-read-table>`_.
+ A fully working real-world example containing both types of configuration can be found `here <https://github.com/snakemake-workflows/rna-seq-star-deseq2>`_.
+
+ ---------------------
+@@ -104,7 +104,7 @@ Instead, for data provenance and reproducibility reasons, you are required to pa
+ Validation
+ ----------
+
+-With Snakemake 5.1, it is possible to validate both types of configuration via `JSON schemas <http://json-schema.org>`_.
++With Snakemake 5.1, it is possible to validate both types of configuration via `JSON schemas <https://json-schema.org>`_.
+ The function ``snakemake.utils.validate`` takes a loaded configuration (a config dictionary or a Pandas data frame) and validates it with a given JSON schema.
+ Thereby, the schema can be provided in JSON or YAML format. Also, by using the defaults property it is possible to populate entries with default values. See `jsonschema FAQ on setting default values <https://python-jsonschema.readthedocs.io/en/latest/faq/>`_ for details.
+ In case of the data frame, the schema should model the record that is expected in each row of the data frame.
+@@ -137,7 +137,7 @@ the schema for validating the samples data frame looks like this:
+
+ .. code-block:: yaml
+
+- $schema: "http://json-schema.org/draft-06/schema#"
++ $schema: "https://json-schema.org/draft-06/schema#"
+ description: an entry in the sample sheet
+ properties:
+ sample:
+diff --git a/docs/snakefiles/deployment.rst b/docs/snakefiles/deployment.rst
+index 775a3ff8..4fa0fc93 100644
+--- a/docs/snakefiles/deployment.rst
++++ b/docs/snakefiles/deployment.rst
+@@ -61,8 +61,8 @@ Integrated Package Management
+ -----------------------------
+
+ With Snakemake 3.9.0 it is possible to define isolated software environments per rule.
+-Upon execution of a workflow, the `Conda package manager <http://conda.pydata.org>`_ is used to obtain and deploy the defined software packages in the specified versions. Packages will be installed into your working directory, without requiring any admin/root priviledges.
+-Given that conda is available on your system (see `Miniconda <http://conda.pydata.org/miniconda.html>`_), to use the Conda integration, add the ``--use-conda`` flag to your workflow execution command, e.g. ``snakemake --cores 8 --use-conda``.
++Upon execution of a workflow, the `Conda package manager <https://conda.pydata.org>`_ is used to obtain and deploy the defined software packages in the specified versions. Packages will be installed into your working directory, without requiring any admin/root priviledges.
++Given that conda is available on your system (see `Miniconda <https://conda.pydata.org/miniconda.html>`_), to use the Conda integration, add the ``--use-conda`` flag to your workflow execution command, e.g. ``snakemake --cores 8 --use-conda``.
+ When ``--use-conda`` is activated, Snakemake will automatically create software environments for any used wrapper (see :ref:`snakefiles-wrappers`).
+ Further, you can manually define environments via the ``conda`` directive, e.g.:
+
+diff --git a/docs/snakefiles/modularization.rst b/docs/snakefiles/modularization.rst
+index 399377fe..fef0453d 100644
+--- a/docs/snakefiles/modularization.rst
++++ b/docs/snakefiles/modularization.rst
+@@ -52,7 +52,7 @@ The `Snakemake Wrapper Repository`_ is meant as a collaborative project and pull
+ Common-Workflow-Language (CWL) support
+ --------------------------------------
+
+-With Snakemake 4.8.0, it is possible to refer to `CWL <http://www.commonwl.org/>`_ tool definitions in rules instead of specifying a wrapper or a plain shell command.
++With Snakemake 4.8.0, it is possible to refer to `CWL <https://www.commonwl.org/>`_ tool definitions in rules instead of specifying a wrapper or a plain shell command.
+ A CWL tool definition can be used as follows.
+
+ .. code-block:: python
+@@ -75,7 +75,7 @@ Snakemake will execute the rule by invoking `cwltool`, which has to be available
+ When using in combination with :ref:`--use-singularity <singularity>`, Snakemake will instruct `cwltool` to execute the command via Singularity in user space.
+ Otherwise, `cwltool` will in most cases use a Docker container, which requires Docker to be set up properly.
+
+-The advantage is that predefined tools available via any `repository of CWL tool definitions <http://www.commonwl.org/#Repositories_of_CWL_Tools_and_Workflows>`_ can be used in any supporting workflow management system.
++The advantage is that predefined tools available via any `repository of CWL tool definitions <https://www.commonwl.org/#Repositories_of_CWL_Tools_and_Workflows>`_ can be used in any supporting workflow management system.
+ In contrast to a :ref:`Snakemake wrapper <snakefiles-wrappers>`, CWL tool definitions are in general not suited to alter the behavior of a tool, e.g., by normalizing output names or special input handling.
+ As you can see in comparison to the analog :ref:`wrapper declaration <snakefiles-wrappers>` above, the rule becomes slightly more verbose, because input, output, and params have to be dispatched to the specific expectations of the CWL tool definition.
+
+diff --git a/docs/snakefiles/remote_files.rst b/docs/snakefiles/remote_files.rst
+index ca46f900..6915103c 100644
+--- a/docs/snakefiles/remote_files.rst
++++ b/docs/snakefiles/remote_files.rst
+@@ -32,7 +32,7 @@ Amazon Simple Storage Service (S3)
+
+ This section describes usage of the S3 RemoteProvider, and also provides an intro to remote files and their usage.
+
+-It is important to note that you must have credentials (``access_key_id`` and ``secret_access_key``) which permit read/write access. If a file only serves as input to a Snakemake rule, read access is sufficient. You may specify credentials as environment variables or in the file ``=/.aws/credentials``, prefixed with ``AWS_*``, as with a standard `boto config <http://boto.readthedocs.org/en/latest/boto_config_tut.html>`_. Credentials may also be explicitly listed in the ``Snakefile``, as shown below:
++It is important to note that you must have credentials (``access_key_id`` and ``secret_access_key``) which permit read/write access. If a file only serves as input to a Snakemake rule, read access is sufficient. You may specify credentials as environment variables or in the file ``=/.aws/credentials``, prefixed with ``AWS_*``, as with a standard `boto config <https://boto.readthedocs.org/en/latest/boto_config_tut.html>`_. Credentials may also be explicitly listed in the ``Snakefile``, as shown below:
+
+ For the Amazon S3 and Google Cloud Storage providers, the sub-directory used must be the bucket name.
+
+@@ -264,7 +264,7 @@ Web addresses must be specified without protocol, so if your URI looks like this
+
+ .. code-block:: text
+
+- http://server3.example.com/path/to/myfile.tar.gz
++ https://server3.example.com/path/to/myfile.tar.gz
+
+ The URI used in the ``Snakefile`` must look like this:
+
+diff --git a/docs/snakefiles/rules.rst b/docs/snakefiles/rules.rst
+index 04ddbe31..99fec6f5 100644
+--- a/docs/snakefiles/rules.rst
++++ b/docs/snakefiles/rules.rst
+@@ -14,7 +14,7 @@ Most importantly, a rule can consist of a name (the name is optional and can be
+ output: "path/to/outputfile", "path/to/another/outputfile"
+ shell: "somecommand {input} {output}"
+
+-Inside the shell command, all local and global variables, especially input and output files can be accessed via their names in the `python format minilanguage <http://docs.python.org/py3k/library/string.html#formatspec>`_. Here input and output (and in general any list or tuple) automatically evaluate to a space-separated list of files (i.e. ``path/to/inputfile path/to/other/inputfile``).
++Inside the shell command, all local and global variables, especially input and output files can be accessed via their names in the `python format minilanguage <https://docs.python.org/py3k/library/string.html#formatspec>`_. Here input and output (and in general any list or tuple) automatically evaluate to a space-separated list of files (i.e. ``path/to/inputfile path/to/other/inputfile``).
+ From Snakemake 3.8.0 on, adding the special formatting instruction ``:q`` (e.g. ``"somecommand {input:q} {output:q}")``) will let Snakemake quote each of the list or tuple elements that contains whitespace.
+ Instead of a shell command, a rule can run some python code to generate the output:
+
+@@ -117,7 +117,7 @@ Finally, you can also define global wildcard constraints that apply for all rule
+ rule b:
+ ...
+
+-See the `Python documentation on regular expressions <http://docs.python.org/py3k/library/re.html>`_ for detailed information on regular expression syntax.
++See the `Python documentation on regular expressions <https://docs.python.org/py3k/library/re.html>`_ for detailed information on regular expression syntax.
+
+
+ Aggregation
+@@ -486,7 +486,7 @@ Inside the script, you have access to an object ``snakemake`` that provides acce
+ Apart from Python scripts, this mechanism also allows you to integrate R_ and R Markdown_ scripts with Snakemake, e.g.
+
+ .. _R: https://www.r-project.org
+-.. _Markdown: http://rmarkdown.rstudio.com
++.. _Markdown: https://rmarkdown.rstudio.com
+
+ .. code-block:: python
+
+diff --git a/docs/tutorial/additional_features.rst b/docs/tutorial/additional_features.rst
+index 54d1178e..af3973c7 100644
+--- a/docs/tutorial/additional_features.rst
++++ b/docs/tutorial/additional_features.rst
+@@ -6,32 +6,32 @@ Additional features
+ .. _Snakemake: https://snakemake.readthedocs.io
+ .. _Snakemake homepage: https://snakemake.readthedocs.io
+ .. _GNU Make: https://www.gnu.org/software/make
+-.. _Python: http://www.python.org
++.. _Python: https://www.python.org
+ .. _BWA: http://bio-bwa.sourceforge.net
+-.. _SAMtools: http://www.htslib.org
+-.. _BCFtools: http://www.htslib.org
+-.. _Pandas: http://pandas.pydata.org
+-.. _Miniconda: http://conda.pydata.org/miniconda.html
+-.. _Conda: http://conda.pydata.org
+-.. _Bash: http://www.tldp.org/LDP/Bash-Beginners-Guide/html
++.. _SAMtools: https://www.htslib.org
++.. _BCFtools: https://www.htslib.org
++.. _Pandas: https://pandas.pydata.org
++.. _Miniconda: https://conda.pydata.org/miniconda.html
++.. _Conda: https://conda.pydata.org
++.. _Bash: https://www.tldp.org/LDP/Bash-Beginners-Guide/html
+ .. _Atom: https://atom.io
+ .. _Anaconda: https://anaconda.org
+-.. _Graphviz: http://www.graphviz.org
++.. _Graphviz: https://www.graphviz.org
+ .. _RestructuredText: https://docutils.sourceforge.io/docs/user/rst/quickstart.html
+ .. _data URI: https://developer.mozilla.org/en-US/docs/Web/HTTP/data_URIs
+-.. _JSON: http://json.org
+-.. _YAML: http://yaml.org
+-.. _DRMAA: http://www.drmaa.org
++.. _JSON: https://json.org
++.. _YAML: https://yaml.org
++.. _DRMAA: https://www.drmaa.org
+ .. _rpy2: https://rpy2.github.io
+ .. _R: https://www.r-project.org
+ .. _Rscript: https://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html
+-.. _PyYAML: http://pyyaml.org
++.. _PyYAML: https://pyyaml.org
+ .. _Docutils: https://docutils.sourceforge.io
+ .. _Bioconda: https://bioconda.github.io
+ .. _Vagrant: https://www.vagrantup.com
+ .. _Vagrant Documentation: https://docs.vagrantup.com
+-.. _Blogpost: http://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html
+-.. _slides: http://slides.com/johanneskoester/deck-1
++.. _Blogpost: https://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html
++.. _slides: https://slides.com/johanneskoester/deck-1
+
+ In the following, we introduce some features that are beyond the scope of above example workflow.
+ For details and even more features, see :ref:`user_manual-writing_snakefiles`, :ref:`project_info-faq` and the command line help (``snakemake --help``).
+@@ -144,7 +144,7 @@ When Snakemake is executed with
+
+ it will automatically create required environments and
+ activate them before a job is executed.
+-It is best practice to specify at least the `major and minor version <http://semver.org/>`_ of any packages
++It is best practice to specify at least the `major and minor version <https://semver.org/>`_ of any packages
+ in the environment definition. Specifying environments per rule in this way has two
+ advantages.
+ First, the workflow definition also documents all used software versions.
+diff --git a/docs/tutorial/advanced.rst b/docs/tutorial/advanced.rst
+index f7ead578..03a91988 100644
+--- a/docs/tutorial/advanced.rst
++++ b/docs/tutorial/advanced.rst
+@@ -6,32 +6,32 @@ Advanced: Decorating the example workflow
+ .. _Snakemake: https://snakemake.readthedocs.io
+ .. _Snakemake homepage: https://snakemake.readthedocs.io
+ .. _GNU Make: https://www.gnu.org/software/make
+-.. _Python: http://www.python.org
++.. _Python: https://www.python.org
+ .. _BWA: http://bio-bwa.sourceforge.net
+-.. _SAMtools: http://www.htslib.org
+-.. _BCFtools: http://www.htslib.org
+-.. _Pandas: http://pandas.pydata.org
+-.. _Miniconda: http://conda.pydata.org/miniconda.html
+-.. _Conda: http://conda.pydata.org
+-.. _Bash: http://www.tldp.org/LDP/Bash-Beginners-Guide/html
++.. _SAMtools: https://www.htslib.org
++.. _BCFtools: https://www.htslib.org
++.. _Pandas: https://pandas.pydata.org
++.. _Miniconda: https://conda.pydata.org/miniconda.html
++.. _Conda: https://conda.pydata.org
++.. _Bash: https://www.tldp.org/LDP/Bash-Beginners-Guide/html
+ .. _Atom: https://atom.io
+ .. _Anaconda: https://anaconda.org
+-.. _Graphviz: http://www.graphviz.org
++.. _Graphviz: https://www.graphviz.org
+ .. _RestructuredText: https://docutils.sourceforge.io/docs/user/rst/quickstart.html
+ .. _data URI: https://developer.mozilla.org/en-US/docs/Web/HTTP/data_URIs
+-.. _JSON: http://json.org
+-.. _YAML: http://yaml.org
+-.. _DRMAA: http://www.drmaa.org
++.. _JSON: https://json.org
++.. _YAML: https://yaml.org
++.. _DRMAA: https://www.drmaa.org
+ .. _rpy2: https://rpy2.github.io
+ .. _R: https://www.r-project.org
+ .. _Rscript: https://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html
+-.. _PyYAML: http://pyyaml.org
++.. _PyYAML: https://pyyaml.org
+ .. _Docutils: https://docutils.sourceforge.io
+ .. _Bioconda: https://bioconda.github.io
+ .. _Vagrant: https://www.vagrantup.com
+ .. _Vagrant Documentation: https://docs.vagrantup.com
+-.. _Blogpost: http://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html
+-.. _slides: http://slides.com/johanneskoester/deck-1
++.. _Blogpost: https://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html
++.. _slides: https://slides.com/johanneskoester/deck-1
+
+ Now that the basic concepts of Snakemake have been illustrated, we can introduce advanced topics.
+
+diff --git a/docs/tutorial/basics.rst b/docs/tutorial/basics.rst
+index cc1cfb45..fe97f775 100644
+--- a/docs/tutorial/basics.rst
++++ b/docs/tutorial/basics.rst
+@@ -6,32 +6,32 @@ Basics: An example workflow
+ .. _Snakemake: https://snakemake.readthedocs.io
+ .. _Snakemake homepage: https://snakemake.readthedocs.io
+ .. _GNU Make: https://www.gnu.org/software/make
+-.. _Python: http://www.python.org
++.. _Python: https://www.python.org
+ .. _BWA: http://bio-bwa.sourceforge.net
+-.. _SAMtools: http://www.htslib.org
+-.. _BCFtools: http://www.htslib.org
+-.. _Pandas: http://pandas.pydata.org
+-.. _Miniconda: http://conda.pydata.org/miniconda.html
+-.. _Conda: http://conda.pydata.org
+-.. _Bash: http://www.tldp.org/LDP/Bash-Beginners-Guide/html
++.. _SAMtools: https://www.htslib.org
++.. _BCFtools: https://www.htslib.org
++.. _Pandas: https://pandas.pydata.org
++.. _Miniconda: https://conda.pydata.org/miniconda.html
++.. _Conda: https://conda.pydata.org
++.. _Bash: https://www.tldp.org/LDP/Bash-Beginners-Guide/html
+ .. _Atom: https://atom.io
+ .. _Anaconda: https://anaconda.org
+-.. _Graphviz: http://www.graphviz.org
++.. _Graphviz: https://www.graphviz.org
+ .. _RestructuredText: https://docutils.sourceforge.io/docs/user/rst/quickstart.html
+ .. _data URI: https://developer.mozilla.org/en-US/docs/Web/HTTP/data_URIs
+-.. _JSON: http://json.org
+-.. _YAML: http://yaml.org
+-.. _DRMAA: http://www.drmaa.org
++.. _JSON: https://json.org
++.. _YAML: https://yaml.org
++.. _DRMAA: https://www.drmaa.org
+ .. _rpy2: https://rpy2.github.io
+ .. _R: https://www.r-project.org
+ .. _Rscript: https://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html
+-.. _PyYAML: http://pyyaml.org
++.. _PyYAML: https://pyyaml.org
+ .. _Docutils: https://docutils.sourceforge.io
+ .. _Bioconda: https://bioconda.github.io
+ .. _Vagrant: https://www.vagrantup.com
+ .. _Vagrant Documentation: https://docs.vagrantup.com
+-.. _Blogpost: http://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html
+-.. _slides: http://slides.com/johanneskoester/deck-1
++.. _Blogpost: https://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html
++.. _slides: https://slides.com/johanneskoester/deck-1
+
+ Please make sure that you have **activated** the environment we created before, and that you have an open terminal in the working directory you have created.
+
+diff --git a/docs/tutorial/setup.rst b/docs/tutorial/setup.rst
+index 32ff8ca3..a098bc28 100644
+--- a/docs/tutorial/setup.rst
++++ b/docs/tutorial/setup.rst
+@@ -4,20 +4,20 @@
+ Setup
+ -----
+
+-.. _Snakemake: http://snakemake.readthedocs.io
+-.. _Snakemake homepage: http://snakemake.readthedocs.io
++.. _Snakemake: https://snakemake.readthedocs.io
++.. _Snakemake homepage: https://snakemake.readthedocs.io
+ .. _GNU Make: https://www.gnu.org/software/make
+-.. _Python: http://www.python.org
++.. _Python: https://www.python.org
+ .. _BWA: http://bio-bwa.sourceforge.net
+-.. _SAMtools: http://www.htslib.org
+-.. _BCFtools: http://www.htslib.org
+-.. _Pandas: http://pandas.pydata.org
+-.. _Miniconda: http://conda.pydata.org/miniconda.html
+-.. _Conda: http://conda.pydata.org
+-.. _Bash: http://www.tldp.org/LDP/Bash-Beginners-Guide/html
++.. _SAMtools: https://www.htslib.org
++.. _BCFtools: https://www.htslib.org
++.. _Pandas: https://pandas.pydata.org
++.. _Miniconda: https://conda.pydata.org/miniconda.html
++.. _Conda: https://conda.pydata.org
++.. _Bash: https://www.tldp.org/LDP/Bash-Beginners-Guide/html
+ .. _Atom: https://atom.io
+-.. _Graphviz: http://www.graphviz.org
+-.. _PyYAML: http://pyyaml.org
++.. _Graphviz: https://www.graphviz.org
++.. _PyYAML: https://pyyaml.org
+ .. _Docutils: https://docutils.sourceforge.io
+ .. _Jinja2: https://jinja.palletsprojects.com
+ .. _NetworkX: https://networkx.github.io
+@@ -26,7 +26,7 @@ Setup
+ .. _Bioconda: https://bioconda.github.io
+ .. _Vagrant: https://www.vagrantup.com
+ .. _Vagrant Documentation: https://docs.vagrantup.com
+-.. _Blogpost: http://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html
++.. _Blogpost: https://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html
+
+ Requirements
+ ::::::::::::
+diff --git a/docs/tutorial/short.rst b/docs/tutorial/short.rst
+index ab4d3a7f..95571f73 100644
+--- a/docs/tutorial/short.rst
++++ b/docs/tutorial/short.rst
+@@ -184,12 +184,12 @@ variants. First, we define a variable
+ at the top of the ``Snakefile``. This serves as a definition of the
+ samples over which we would want to aggregate. In real life, you would
+ want to use an external sample sheet or a `config
+-file <http://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#step-2-config-files>`__
++file <https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#step-2-config-files>`__
+ for things like this.
+
+ For aggregation over many files, Snakemake provides the helper function
+ ``expand`` (see `the
+-docs <http://snakemake.readthedocs.io/en/stable/tutorial/basics.html#step-5-calling-genomic-variants>`__).
++docs <https://snakemake.readthedocs.io/en/stable/tutorial/basics.html#step-5-calling-genomic-variants>`__).
+ Create a rule ``call`` with input files
+
+ - ``fa="data/genome.fa"``
+diff --git a/docs/tutorial/tutorial.rst b/docs/tutorial/tutorial.rst
+index 768ead56..00b655f5 100644
+--- a/docs/tutorial/tutorial.rst
++++ b/docs/tutorial/tutorial.rst
+@@ -4,10 +4,10 @@
+ Snakemake Tutorial
+ ==================
+
+-.. _Snakemake: http://snakemake.readthedocs.io
++.. _Snakemake: https://snakemake.readthedocs.io
+ .. _GNU Make: https://www.gnu.org/software/make
+-.. _Python: http://www.python.org
+-.. _slides: http://slides.com/johanneskoester/snakemake-tutorial
++.. _Python: https://www.python.org
++.. _slides: https://slides.com/johanneskoester/snakemake-tutorial
+ .. _Conda: https://conda.io
+ .. _Singularity: https://www.sylabs.io
+
+diff --git a/snakemake/gui.html b/snakemake/gui.html
+index a9243f3e..c2d30fc4 100644
+--- a/snakemake/gui.html
++++ b/snakemake/gui.html
+@@ -2,13 +2,13 @@
+ <html lang="en">
+ <head>
+ <title>Snakemake</title>
+- <script type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
+- <script type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/d3/3.4.6/d3.min.js"></script>
+- <script type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.1.1/js/bootstrap.min.js"></script>
+- <script type="text/javascript" src="http://cpettitt.github.io/project/dagre-d3/v0.1.5/dagre-d3.js"></script>
+- <script type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.5.4/bootstrap-select.min.js"></script>
+- <link rel="stylesheet" type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.1.1/css/bootstrap.min.css"/>
+- <link rel="stylesheet" type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.5.4/bootstrap-select.min.css"/>
++ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
++ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.4.6/d3.min.js"></script>
++ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.1.1/js/bootstrap.min.js"></script>
++ <script type="text/javascript" src="https://cpettitt.github.io/project/dagre-d3/v0.1.5/dagre-d3.js"></script>
++ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.5.4/bootstrap-select.min.js"></script>
++ <link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.1.1/css/bootstrap.min.css"/>
++ <link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.5.4/bootstrap-select.min.css"/>
+ <style>
+ body {
+ font-family: sans-serif;
+diff --git a/snakemake/io.py b/snakemake/io.py
+index ff149c3c..2b3a30f9 100755
+--- a/snakemake/io.py
++++ b/snakemake/io.py
+@@ -1355,7 +1355,7 @@ def _load_configfile(configpath, filetype="Config"):
+ except ValueError:
+ f.seek(0) # try again
+ try:
+- # From http://stackoverflow.com/a/21912744/84349
++ # From https://stackoverflow.com/a/21912744/84349
+ class OrderedLoader(yaml.Loader):
+ pass
+
+diff --git a/snakemake/remote/NCBI.py b/snakemake/remote/NCBI.py
+index b232dd77..a64428bc 100644
+--- a/snakemake/remote/NCBI.py
++++ b/snakemake/remote/NCBI.py
+@@ -443,7 +443,7 @@ class NCBIHelper(object):
+ def parse_accession_str(self, id_str):
+ """
+ This tries to match an NCBI accession as defined here:
+- http://www.ncbi.nlm.nih.gov/Sequin/acc.html
++ https://www.ncbi.nlm.nih.gov/Sequin/acc.html
+ """
+ m = re.search(
+ r"(?P<accession>(?:[a-zA-Z]{1,6}|NW_|NC_|NM_|NR_)\d{1,10})(?:\.(?P<version>\d+))?(?:\.(?P<file_ext>\S+))?.*",
+@@ -467,7 +467,7 @@ class NCBIHelper(object):
+
+ @staticmethod
+ def _seq_chunks(seq, n):
+- # http://stackoverflow.com/a/312464/190597 (Ned Batchelder)
++ # https://stackoverflow.com/a/312464/190597 (Ned Batchelder)
+ """ Yield successive n-sized chunks from seq."""
+ for i in range(0, len(seq), n):
+ yield seq[i : i + n]
+diff --git a/snakemake/utils.py b/snakemake/utils.py
+index 451c25ca..7edadc2e 100644
+--- a/snakemake/utils.py
++++ b/snakemake/utils.py
+@@ -31,10 +31,10 @@ def validate(data, schema, set_default=True):
+ schema (str): Path to JSON schema used for validation. The schema can also be
+ in YAML format. If validating a pandas data frame, the schema has to
+ describe a row record (i.e., a dict with column names as keys pointing
+- to row values). See http://json-schema.org. The path is interpreted
++ to row values). See https://json-schema.org. The path is interpreted
+ relative to the Snakefile when this function is called.
+ set_default (bool): set default values defined in schema. See
+- http://python-jsonschema.readthedocs.io/en/latest/faq/ for more
++ https://python-jsonschema.readthedocs.io/en/latest/faq/ for more
+ information
+ """
+ try:
+@@ -61,7 +61,7 @@ def validate(data, schema, set_default=True):
+ handlers={"file": lambda uri: _load_configfile(re.sub("^file://", "", uri))},
+ )
+
+- # Taken from http://python-jsonschema.readthedocs.io/en/latest/faq/
++ # Taken from https://python-jsonschema.readthedocs.io/en/latest/faq/
+ def extend_with_default(validator_class):
+ validate_properties = validator_class.VALIDATORS["properties"]
+
+@@ -450,7 +450,7 @@ def update_config(config, overwrite_config):
+ """Recursively update dictionary config with overwrite_config.
+
+ See
+- http://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth
++ https://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth
+ for details.
+
+ Args:
+@@ -477,7 +477,7 @@ def available_cpu_count():
+ when the cpuset(7) mechanism is in use, as is the case on some cluster
+ systems.
+
+- Adapted from http://stackoverflow.com/a/1006301/715090
++ Adapted from https://stackoverflow.com/a/1006301/715090
+ """
+ try:
+ with open("/proc/self/status") as f:
+diff --git a/versioneer.py b/versioneer.py
+index 64fea1c8..a9dba122 100644
+--- a/versioneer.py
++++ b/versioneer.py
+@@ -1752,7 +1752,7 @@ def do_setup():
+ except EnvironmentError:
+ pass
+ # That doesn't cover everything MANIFEST.in can do
+- # (http://docs.python.org/2/distutils/sourcedist.html#commands), so
++ # (https://docs.python.org/2/distutils/sourcedist.html#commands), so
+ # it might give some false negatives. Appending redundant 'include'
+ # lines is safe, though.
+ if "versioneer.py" not in simple_includes:
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,5 @@ local_javascript.patch
0009-skip-test-without-google-cloud-sdk.patch
python3.patch
workaround_sphinx_issue.patch
+link_security.patch
+bug322_cluster_sync.patch
=====================================
debian/patches/workaround_sphinx_issue.patch
=====================================
@@ -1,12 +1,14 @@
-From: "Rebecca N. Palmer" <rebecca_palmer at zoho.com>
-Date: Wed, 8 Apr 2020 22:13:19 +0100
+Description: Exclude common.py:lazy_property from documentation
+
+Needed as Sphinx 2 can't process it
+
+This is obviously not an ideal fix, but it's an internal class with little
+documentation to begin with:
+https://snakemake.readthedocs.io/en/stable/api_reference/internal/snakemake.html#snakemake.common.lazy_property
+
+Author: Rebecca N. Palmer <rebecca_palmer at zoho.com>
Bug-Debian: https://bugs.debian.org/955056
-Description: An upstream comment says common.py:lazy_property is the problem item,
- and excluding that from the documentation does make Sphinx succeed (I
- haven't tested a whole build):
- .
- This is obviously not an ideal fix, but it's an internal class with little
- documentation to begin with: https://snakemake.readthedocs.io/en/stable/api_reference/internal/snakemake.html#snakemake.common.lazy_property
+Forwarded: https://github.com/snakemake/snakemake/issues/296#issuecomment-611197453
--- a/docs/conf.py
+++ b/docs/conf.py
=====================================
debian/rules
=====================================
@@ -7,7 +7,7 @@ export HOME=$(CURDIR)/fakehome
export PYBUILD_NAME=snakemake
export PYBUILD_DESTDIR_python3=debian/snakemake
export PYBUILD_BEFORE_TEST_python3=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir}
-export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container and not test_cluster_sync'
+export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container'
# test_report
# test_ancient
@@ -21,7 +21,6 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -n auto -k
# test_env_modules relies on "module load" which is not packaged for Debian
# test_archive uses conda
# test_container uses docker://bash
-# test_cluster_sync is broken (https://github.com/snakemake/snakemake/issues/322)
export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests {dir}/tests/test_filegraph/.snakemake/ {dir}/tests/linting/*/.snakemake/
=====================================
debian/tests/run-unit-test
=====================================
@@ -17,5 +17,5 @@ cd "${AUTOPKGTEST_TMP}"
export HOME="${AUTOPKGTEST_TMP}"
-python3 -m pytest -v ${ROOT}/tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_singularity and not test_singularity_conda and not test_cwl_singularity and not test_cwl and not test_url_include and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container and not test_cluster_sync'
+python3 -m pytest -v ${ROOT}/tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_singularity and not test_singularity_conda and not test_cwl_singularity and not test_cwl and not test_url_include and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container'
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/e7d154fa5c24b5873740cbdafc72920f1660f3c9...7d50f8d318478b6bb767b008c540da954f4fc92a
--
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/e7d154fa5c24b5873740cbdafc72920f1660f3c9...7d50f8d318478b6bb767b008c540da954f4fc92a
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