[med-svn] [Git][med-team/bcbio][master] Updates.

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
915f9844 by Steffen Moeller at 2020-07-20T00:29:02+02:00
Updates.

- - - - -


2 changed files:

- debian/TODO
- debian/control


Changes:

=====================================
debian/TODO
=====================================
@@ -101,14 +101,6 @@ package libjs-scribl (rejected)
     A surprisingly neat JavaScript library to show genomic features
        Needed for DFSG-compliance of seqcluster
 
-Package MultiQC (in crash space) (rejected from new)
-   https://salsa.debian.org/med-team/multiqc
-     Addressed https://github.com/ewels/MultiQC/issues/800 by substuting
-     with references to CDNs instead of local files.
-     The package was placed into contrib because of the dependency of its
-     reports on external sources. For that reason and the remote depenency
-     on ViennaRNA via seqcluster, also bcbio will be in contrib.
-     
 Packages just waiting for someone addressing the last mile for the upload
 -------------------------------------------------------------------------
 


=====================================
debian/control
=====================================
@@ -21,33 +21,34 @@ Build-Depends: debhelper-compat (= 12),
                python3-psutil,
                python3-joblib,
 # for testing
-               atropos,
-               bedtools,
-               biobambam2,
-               gffread,
-               grabix,
-               hisat2,
-#               mosdepth, # missing
-               perl,
-               picard,
-               python3-biopython,
-               python3-cyvcf2,
-               python3-geneimpacts,
-               python3-logbook,
-               python3-nose,
-               python3-requests,
-               python3-pytest,
-               python3-pytest-mock,
-               bcftools,
-               rna-star,
-               salmon,
-               samblaster,
-               samtools,
-               seqtk,
-               tabix,
-               tophat-recondition,
-               wham-align,
-               xonsh,
+               atropos <!nocheck>,
+               bedtools <!nocheck>,
+               biobambam2 <!nocheck>,
+               gffread <!nocheck>,
+               grabix <!nocheck>,
+               hisat2 <!nocheck>,
+#               mosdepth <!nocheck>, # missing
+               multiqc <!nocheck>,
+               perl <!nocheck>,
+               picard <!nocheck>,
+               python3-biopython <!nocheck>,
+               python3-cyvcf2 <!nocheck>,
+               python3-geneimpacts <!nocheck>,
+               python3-logbook <!nocheck>,
+               python3-nose <!nocheck>,
+               python3-requests <!nocheck>,
+               python3-pytest <!nocheck>,
+               python3-pytest-mock <!nocheck>,
+               bcftools <!nocheck>,
+               rna-star <!nocheck>,
+               salmon <!nocheck>,
+               samblaster <!nocheck>,
+               samtools <!nocheck>,
+               seqtk <!nocheck>,
+               tabix <!nocheck>,
+               tophat-recondition <!nocheck>,
+               wham-align <!nocheck>,
+               xonsh <!nocheck>,
 # documentation
                python3-sphinx
 Standards-Version: 4.5.0
@@ -73,13 +74,15 @@ Depends: ${python3:Depends},
          python3-six,
          python3-tornado
 Recommends:
+         multiqc,
          python3-arrow,
          python3-geneimpacts,
          python3-h5py,
          python3-pyvcf,
          python3-seqcluster,
          python3-statsmodels,
-         python3-tabulate
+         python3-tabulate,
+         vt
 Suggests:
          bcbio-doc,
          python3-bioblend,



View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/915f9844da6f8643b8f2bc9923dba096659eb08c

-- 
View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/915f9844da6f8643b8f2bc9923dba096659eb08c
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