[med-svn] [Git][med-team/bcbio][master] 2 commits: Removed obsolete patch

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
500c1dd9 by Steffen Moeller at 2021-05-07T22:31:43+02:00
Removed obsolete patch

- - - - -
793c330d by Steffen Moeller at 2021-05-07T23:17:42+02:00
Update of dependencies

- - - - -


5 changed files:

- debian/README.Debian
- debian/changelog
- debian/control
- − debian/patches/collectionsAbc.patch
- debian/patches/series


Changes:

=====================================
debian/README.Debian
=====================================
@@ -5,4 +5,7 @@ This package builds and tests fine, but the documentation is not yet packaged.
 
 Please be aware of related Debian packages for toil and cwltool.
 
+The package "tophat" was removed from Debian since the developer of
+tophat considered the tool outdated. This affects the "singleended" test of bcbio, though.
+
  -- Steffen Moeller   Mon, 21 Jan 2019 21:30:11 +0100


=====================================
debian/changelog
=====================================
@@ -2,6 +2,8 @@ bcbio (1.2.8-1) UNRELEASED; urgency=medium
 
   * New upstream version.
   * Standards-Version: 4.5.1 (routine-update)
+  * Removed now obsolete patch on abc collections
+  * Updated dependencies
 
  -- Steffen Moeller <moeller at debian.org>  Fri, 07 May 2021 20:29:57 +0200
 


=====================================
debian/control
=====================================
@@ -27,6 +27,7 @@ Build-Depends: debhelper-compat (= 13),
                bedtools <!nocheck>,
                biobambam2 <!nocheck>,
                bowtie2 <!nocheck>,
+               bwa <!nocheck>,
                cnvkit <!nocheck>,
                fastqc <!nocheck>,
                freebayes <!nocheck>,
@@ -67,6 +68,7 @@ Build-Depends: debhelper-compat (= 13),
                samtools <!nocheck>,
                seqan-apps <!nocheck>,
                seqtk <!nocheck>,
+               snpeff <!nocheck>,
                subread <!nocheck>,
                tabix <!nocheck>,
                tophat-recondition <!nocheck>,
@@ -118,6 +120,7 @@ Recommends: cnvkit,
             r-bioc-purecn,
             r-bioc-titancna,
             seqan-apps,
+            snpeff,
             vcfanno,
             vt
 Suggests: bcbio-doc,
@@ -142,6 +145,7 @@ Depends: ${python3:Depends},
          ${misc:Depends},
          python3-bcbio
 Recommends: bcftools,
+            bwa,
             cnvkit,
             cufflinks,
             delly,


=====================================
debian/patches/collectionsAbc.patch deleted
=====================================


=====================================
debian/patches/series
=====================================
@@ -4,6 +4,5 @@ pytest2to3.patch
 do_not_use_git.patch
 pythonpaths.patch
 hts_nim_tools.patch
-collectionsAbc.patch
 cnvkitPath.patch
 fixeFreetypePreload.patch



View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/cd8feac301800694e286f39f4104597b70d1d857...793c330de6805efac17fc4527d388778f5f52081

-- 
View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/cd8feac301800694e286f39f4104597b70d1d857...793c330de6805efac17fc4527d388778f5f52081
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