[med-svn] [Git][med-team/bcbio][master] Update to d/TODO
Steffen Möller
gitlab at salsa.debian.org
Wed Nov 4 19:03:09 GMT 2020
Steffen Möller pushed to branch master at Debian Med / bcbio
Commits:
83db5e8f by Steffen Moeller at 2020-11-04T20:02:55+01:00
Update to d/TODO
- - - - -
2 changed files:
- debian/TODO
- debian/control
Changes:
=====================================
debian/TODO
=====================================
@@ -45,7 +45,7 @@ convinced that this is no longer required.
#py # conda-specific
python-dateutil >=2.5.0 # likely obsolete?
pyyaml https://pyyaml.org/wiki/PyYAML
- seqcluster # not yet in new
+ python3-seqcluster # to be reuploaded
To be packaged
fadapa https://github.com/fadapa/fadapa
pycrypto
@@ -58,6 +58,7 @@ convinced that this is no longer required.
pytest-mock
pytest-cov
seaborn # not called directly?
+ viennarna dragged in via python3-seqcluster
yamllint
Already a dependency
pytest # an implicit python build dependency
@@ -81,6 +82,7 @@ convinced that this is no longer required.
pyvcf
requests
scipy >=1.3.0
+ seqcluster
statsmodels
tabulate
toolz
@@ -104,73 +106,29 @@ package libjs-scribl (rejected)
Packages just waiting for someone addressing the last mile for the upload
-------------------------------------------------------------------------
-package viennarna (in crash space)
- https://github.com/ViennaRNA/ViennaRNA
- https://salsa.debian.org/med-team/vienna-rna/blob/master/debian/changelog
- The package now has a custom license file - redistributable but non-free.
- Needed for testing seqcluster.
- Python and Perl packages are not tested, yet, not needed for seqcluster
-dh_auto_install
- Package likely to be uploadable to non-free. Final checks needed.
- Documentation no longer builds with 2.4.14 would be nice to reactivate but not ultimately important for first upload.
-
package pyomo (in crash space)
https://github.com/Pyomo/pyomo
https://salsa.debian.org/science-team/pyomo
needed by optitype
Status: Builds if errors in build time tests will be ignored
+ gjh_asl_json recently added to archive
-package python-seqcluster (in crash space)
- https://github.com/lpantano/seqcluster/
- https://salsa.debian.org/med-team/python-seqcluster
- The Python3 transition seems fine now.
- The package needs RNAfold fof the ViennaRNA package for testing. Otherwise it stalls without an error message.
- Dependencies are incomplete / an update wrecked the one immaculate testing.
- When grepping for "conda install":
- ./doc/source/installation.rst: ~/install/seqcluster/anaconda/conda install seqcluster seqbuster bedtools samtools pip nose numpy scipy pandas pyvcf -c bioconda
- ./Dockerfile: conda install --yes -c conda-forge -c bioconda scipy seqcluster bedtools samtools pip nose setuptools -q && \
- ./.travis.yml:- conda install --yes -c conda-forge -c bioconda memory_profiler openjdk pysam pybedtools pandas numpy biopython progressbar2 pyyaml bedtools samtools mirtop viennarna -q
- so, for some successful testing it seems like we need viennarna, still. That is not yet in the distribution. If truly dependending on it then bcbio ends up in contrib.
-
- seqcluster accepted a patch to eliminate a "Free as in beer" graph library from its source tree at ./misc/js/amcharts.js. These are now references to the online location in a CDN.
-
-
- Additional requirements:
- python3-pytz ----> packaged but under the name python3-tz
-
- And there are R packages that should be recommended at least (from https://github.com/lpantano/seqcluster/blob/master/scripts/install_libraries.R)
- # We cover all CRAN packages
- # Most BioC packages are missing - even edgeR ? :
- apparently optional for bcbio: r-bioc-edgeR - missing
- apparently optional for bcbio: r-bioc-HTSFilter - Depends DESeq and edgeR which both in turn depend locfit which makes all non-free
- apparently optional for bcbio: r-bioc-DEGreport - all pre-depends except edgeR are in new
- # novel packages
- apparently optional for bcbio: install.github("hbc/CHBUtils") - Uploaded to new as r-other-chbutils_0.1+git20171026.a226cee-1
- apparently optional for bcbio: r-bioc-isomiRs - (needs r-bioc-DEGreport) all pre-depends except edgeR are in new
- apparently optional for bcbio: install_github('rstudio/rmarkdown') -- this may be the same we have from CRAN - not checked
+package python-seqcluster (to be reuploaded)
Packages presumed easy to package
---------------------------------
-package gjh_asl_json
- https://github.com/ghackebeil/gjh_asl_json
- needed by pyomo for testing
package hts_nim_tools
https://github.com/brentp/hts-nim-tools
Likely addressed with the other efforts on nim behind mosdepth
+ salsa
package "asl solver"
http://www.ampl.com/netlib/ampl/solvers.tgz
needed by gjh_asl_json
-r-bioc-edgeR
- https://tracker.debian.org/pkg/r-bioc-edger
- This was removed from buster in February - a bit of a bummer, I tend to think
- https://salsa.debian.org/r-pkg-team/r-bioc-edger
- https://bioconductor.org/packages/release/bioc/html/edgeR.html
- Needed by seqcluster
r-bioc-HTSFilter
https://bioconductor.org/packages/release/bioc/html/HTSFilter.html
@@ -186,11 +144,6 @@ r-bioc-DEGreport
Packages of importance for basic NGS workflows with motivation beyond bcbio
---------------------------------------------------------------------------
-package mosdepth
- https://salsa.debian.org/med-team/mosdepth
- several nim libraries are needed. These have all been addressed on https://salsa.debian.org/nim-team
- of which the first already is in the new queue
-
package oncofuse
https://salsa.debian.org/med-team/oncofuse
Stuck over typical Java issue
=====================================
debian/control
=====================================
@@ -27,7 +27,7 @@ Build-Depends: debhelper-compat (= 13),
gffread <!nocheck>,
grabix <!nocheck>,
hisat2 <!nocheck>,
-# mosdepth <!nocheck>, # missing
+ mosdepth <!nocheck>,
multiqc <!nocheck>,
perl <!nocheck>,
libpicard-java <!nocheck>,
@@ -74,6 +74,7 @@ Depends: ${python3:Depends},
python3-six,
python3-tornado
Recommends:
+ mosdepth,
multiqc,
python3-arrow,
python3-geneimpacts,
View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/83db5e8f405d4b774235f814a7edbd6020aa15aa
--
View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/83db5e8f405d4b774235f814a7edbd6020aa15aa
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