[med-svn] [Git][med-team/trinityrnaseq][master] 2 commits: d/control: move many deps of the binary package to recommends/suggests. As not...

[Michael R. Crusoe (@crusoe)]

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


Commits:
e79a057e by Michael R. Crusoe at 2023-09-13T19:56:58+02:00
d/control: move many deps of the binary package to recommends/suggests. As not all deps are needed for all usages, this enables utilitly on architectures where some deps are not available.

- - - - -
f512d7e5 by Michael R. Crusoe at 2023-09-13T22:02:31+02:00
routine-update: Ready to upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/tests/control
- debian/tests/run-tests


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+trinityrnaseq (2.15.1+dfsg-2) unstable; urgency=medium
+
+  * d/control: move many deps of the binary package to recommends/suggests.
+               As not all deps are needed for all usages, this enables
+               usage on architectures where some deps are not available.
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Wed, 13 Sep 2023 22:02:31 +0200
+
 trinityrnaseq (2.15.1+dfsg-1) unstable; urgency=medium
 
   [ Michael R. Crusoe ]


=====================================
debian/control
=====================================
@@ -32,47 +32,47 @@ Depends: ${shlibs:Depends},
          samtools,
          jellyfish,
          r-base-core,
-         r-cran-cluster,
-         r-bioc-qvalue,
          rsem,
          berkeley-express,
          trimmomatic,
-         transdecoder,
          parafly,
-         curl,
-         salmon,
-         python3-numpy,
          ncbi-blast+,
          python3,
-         r-cran-readr,
-         r-bioc-edger,
-         r-bioc-deseq2,
-         r-bioc-rots,
-         r-cran-fastcluster,
          liburi-perl,
-         r-cran-ape,
-         r-bioc-ctc,
-         r-cran-gplots,
-         r-bioc-biobase,
-         r-bioc-goseq,
-         r-bioc-tximport,
          python3-htseq,
-         rna-star,
-         gmap,
-         hisat2,
          subread,
-         kallisto,
-         python3-hisat2,
-         r-cran-argparse,
-         r-cran-goplot,
-         r-bioc-dexseq
-#         r-bioc-glimma
+         kallisto
 Recommends: ${java:Recommends},
+            curl,
             trinityrnaseq-examples,
-            r-cran-tidyverse,
             picard-tools,
-            tabix
+            tabix,
+            gmap,
+            salmon,
+            rna-star,
+            hisat2,
+            r-cran-tidyverse,
+            r-cran-readr,
+            r-bioc-edger,
+            r-bioc-deseq2,
+            r-bioc-rots,
+            r-cran-cluster,
+            r-cran-fastcluster,
+            r-bioc-ctc,
+            r-bioc-goseq,
+            r-cran-goplot,
+            r-cran-gplots,
+            r-bioc-dexseq,
+            r-cran-ape,
+            r-bioc-biobase,
+            r-bioc-qvalue,
+            r-cran-argparse,
+            r-cran-kernsmooth,
+            python3-numpy,
+            python3-hisat2
 Suggests: collectl,
+          transdecoder,
+          r-bioc-tximport,
           r-bioc-tximportdata
 Description: RNA-Seq De novo Assembly
  Trinity represents a novel method for the efficient and robust de novo


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
 Tests: run-tests
-Depends: trinityrnaseq, trinityrnaseq-examples, r-cran-tidyverse, libpicard-java
+Depends: trinityrnaseq, trinityrnaseq-examples, r-cran-tidyverse, libpicard-java, salmon, r-bioc-edger, r-bioc-deseq2, r-cran-cluster, r-bioc-qvalue, r-cran-fastcluster, r-bioc-goseq, r-cran-argparse, r-cran-goplot, r-cran-kernsmooth, hisat2, python3-hisat2, r-bioc-dexseq
 Restrictions: skip-not-installable, allow-stderr


=====================================
debian/tests/run-tests
=====================================
@@ -15,6 +15,7 @@ rm -f trinityrnaseq/sample_data
 cp -rs /usr/share/trinityrnaseq/sample_data trinityrnaseq/
 cp -rs /usr/share/trinityrnaseq/trinity_ext_sample_data trinityrnaseq/
 rm trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/S-Lap3_flush/st.fasta
+
 cd trinityrnaseq/sample_data
 LD_PRELOAD= make test_all
 cd ../trinity_ext_sample_data



View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/f29217285ea0f7de3276eeb05ab42f371117c437...f512d7e5768e7af193ee6db1b69fbe569d82e4c3

-- 
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/f29217285ea0f7de3276eeb05ab42f371117c437...f512d7e5768e7af193ee6db1b69fbe569d82e4c3
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