[med-svn] [Git][med-team/trinityrnaseq][master] 2 commits: Enable more features and tests with r-cran-{argparse, dexseq} & tabix

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / trinityrnaseq


Commits:
c848a047 by Michael R. Crusoe at 2020-10-09T10:46:51+02:00
Enable more features and tests with r-cran-{argparse,dexseq} & tabix

- - - - -
c450962e by Michael R. Crusoe at 2020-10-09T15:17:31+02:00
release 2.11.0+dfsg-1

- - - - -


6 changed files:

- debian/changelog
- debian/control
- debian/patches/series
- debian/patches/skip_blat
- − debian/patches/skip_r-bioc-dexseq
- − debian/patches/skip_r-cran-argpase


Changes:

=====================================
debian/changelog
=====================================
@@ -1,7 +1,6 @@
-trinityrnaseq (2.11.0+dfsg-1) UNRELEASED; urgency=medium
+trinityrnaseq (2.11.0+dfsg-1) unstable; urgency=medium
 
   [ Andreas Tille ]
-  * Team upload.
   * Fix gcc-10 build issue
     Closes: #966876
   * debhelper-compat 13 (routine-update)
@@ -9,14 +8,14 @@ trinityrnaseq (2.11.0+dfsg-1) UNRELEASED; urgency=medium
     *.jars
   * Remove redundant debian/gbp.conf
   * Remove __pycache__ from installed package
-  FIXME: seqtk-trinity is missing and thus autopkgtest fails
 
   [ Michael R. Crusoe ]
   * Correct location of bamsifter installation
   * debian/patches/fix_system_paths: fix expected path for ParaFly
   * debian/patches/update-paths: fix paths to Butterfly.jar
+  * Enable more features and tests with r-cran-{argparse,dexseq} & tabix
 
- -- Andreas Tille <tille at debian.org>  Wed, 05 Aug 2020 12:44:59 +0200
+ -- Michael R. Crusoe <crusoe at debian.org>  Fri, 09 Oct 2020 15:13:36 +0200
 
 trinityrnaseq (2.10.0+dfsg-1) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -37,10 +37,11 @@ Build-Depends: debhelper-compat (= 13),
                hisat2,
                subread,
                kallisto,
-               python3-hisat2
-#               r-cran-argparse,
+               python3-hisat2,
+               r-cran-argparse,
+               r-bioc-dexseq,
+               tabix
 #               r-cran-goplot,
-#               r-bioc-dexseq,
 #               r-bioc-glimma,
 #               r-bioc-tximportdata
 Standards-Version: 4.5.0
@@ -92,15 +93,16 @@ Depends: ${shlibs:Depends},
          hisat2,
          subread,
          kallisto,
-         python3-hisat2
-#         r-cran-argparse,
-#         r-cran-goplot,
+         python3-hisat2,
+         r-cran-argparse,
+         r-cran-goplot
 #         r-bioc-dexseq,
 #         r-bioc-glimma
 Recommends: ${java:Recommends},
             trinityrnaseq-examples,
             r-cran-tidyverse,
-            picard-tools
+            picard-tools,
+            tabix
 Suggests: collectl,
           r-bioc-tximportdata
 Description: RNA-Seq De novo Assembly


=====================================
debian/patches/series
=====================================
@@ -15,8 +15,6 @@ seqtk-trinity-hardening
 skip_gatk_test
 skip_tximportData_tests
 submake
-skip_r-cran-argpase
-skip_r-bioc-dexseq
 skip_blat
 fix-gcc-10.patch
 bamsifter_build


=====================================
debian/patches/skip_blat
=====================================
@@ -2,9 +2,9 @@ Author: Michael R. Crusoe <michael.crusoe>
 Description: skip tests with a dependency on blat
 --- trinityrnaseq.orig/trinity_ext_sample_data/Makefile
 +++ trinityrnaseq/trinity_ext_sample_data/Makefile
-@@ -9,8 +9,7 @@
- test_PtR \
+@@ -11,8 +11,7 @@
  test_SuperTranscript \
+ test_GOplot \
  test_TPM_weighted_gene_length \
 -test_ExN50 \
 -test_Assembly_DiffReadFormattings


=====================================
debian/patches/skip_r-bioc-dexseq deleted
=====================================
@@ -1,12 +0,0 @@
-Author: Michael R. Crusoe <michael.crusoe>
-Description: skip tests with a dependency on r-bioc-dexseq
---- trinityrnaseq.orig/trinity_ext_sample_data/Makefile
-+++ trinityrnaseq/trinity_ext_sample_data/Makefile
-@@ -7,7 +7,6 @@
- test_GOSeq_trinotate_pipe \
- test_profiling_report \
- test_PtR \
--test_DTU \
- test_SuperTranscript \
- test_TPM_weighted_gene_length \
- test_ExN50 \


=====================================
debian/patches/skip_r-cran-argpase deleted
=====================================
@@ -1,21 +0,0 @@
-Author: Michael R. Crusoe <michael.crusoe>
-Description: skip tests with a dependency on r-cran-argparse
---- trinityrnaseq.orig/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Makefile
-+++ trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Makefile
-@@ -1,5 +1,5 @@
- 
--DIRS = Spombe_runGOseqOnly test_GOplot Spombe_analyzeDiffExprWithGOseq
-+DIRS = Spombe_runGOseqOnly Spombe_analyzeDiffExprWithGOseq
- 
- 
- test:
---- trinityrnaseq.orig/trinity_ext_sample_data/Makefile
-+++ trinityrnaseq/trinity_ext_sample_data/Makefile
-@@ -9,7 +9,6 @@
- test_PtR \
- test_DTU \
- test_SuperTranscript \
--test_GOplot \
- test_TPM_weighted_gene_length \
- test_ExN50 \
- test_Assembly_DiffReadFormattings



View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/6c20b127f9edc81ce924ae43bd7782fb4d8e9412...c450962e5f0a2c6200d46bfbb8e0bf1b8a796346

-- 
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/6c20b127f9edc81ce924ae43bd7782fb4d8e9412...c450962e5f0a2c6200d46bfbb8e0bf1b8a796346
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