[med-svn] [Git][med-team/trinityrnaseq][master] 15 commits: r-cran-argparse
Michael R. Crusoe
gitlab at salsa.debian.org
Mon Apr 27 17:15:20 BST 2020
Michael R. Crusoe pushed to branch master at Debian Med / trinityrnaseq
Commits:
1e726c88 by Michael R. Crusoe at 2020-04-27T08:27:06+02:00
r-cran-argparse
- - - - -
613e0394 by Michael R. Crusoe at 2020-04-27T10:29:02+02:00
r-cran-goplot is also needed
- - - - -
3eaa7162 by Michael R. Crusoe at 2020-04-27T10:48:49+02:00
Install trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl
- - - - -
cb8682cc by Michael R. Crusoe at 2020-04-27T11:07:27+02:00
Install trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py
- - - - -
f3c8024a by Michael R. Crusoe at 2020-04-27T12:06:59+02:00
r-bioc-dexseq too
- - - - -
431bf5ea by Michael R. Crusoe at 2020-04-27T12:40:25+02:00
python3-hisat2 needed for hisat2_extract_splice_sites.py
- - - - -
eefd1895 by Michael R. Crusoe at 2020-04-27T13:10:36+02:00
Install PyLib/Pipeliner.py
- - - - -
887187f6 by Michael R. Crusoe at 2020-04-27T13:37:51+02:00
Set PICARD_HOME default of /usr/share/java
- - - - -
d726fbcf by Michael R. Crusoe at 2020-04-27T13:41:14+02:00
Skip tests that require GATK4 until it gets packaged
- - - - -
7645c287 by Michael R. Crusoe at 2020-04-27T14:09:19+02:00
r-bioc-glimma
- - - - -
3d0dec25 by Michael R. Crusoe at 2020-04-27T14:22:11+02:00
Skip tests that require r-bioc-tximportdata
- - - - -
8c220e5b by Michael R. Crusoe at 2020-04-27T14:54:39+02:00
r-cran-readr
- - - - -
dbc1d9e3 by Michael R. Crusoe at 2020-04-27T14:55:59+02:00
debian/patches/submake: use $(MAKE) consistently
- - - - -
8aa33ac6 by Michael R. Crusoe at 2020-04-27T14:58:25+02:00
add another LD_PRELOAD clear
- - - - -
dd9ca55f by Michael R. Crusoe at 2020-04-27T17:26:05+02:00
Skip the remaining tests waiting for new packages
- - - - -
13 changed files:
- debian/changelog
- debian/control
- debian/patches/fix_system_paths
- debian/patches/series
- + debian/patches/skip_blat
- + debian/patches/skip_gatk_test
- + debian/patches/skip_r-bioc-dexseq
- + debian/patches/skip_r-cran-argpase
- + debian/patches/skip_tximportData_tests
- + debian/patches/submake
- debian/tests/control
- debian/tests/run-tests
- debian/trinityrnaseq.install
Changes:
=====================================
debian/changelog
=====================================
@@ -5,8 +5,9 @@ trinityrnaseq (2.10.0+dfsg-1) UNRELEASED; urgency=medium
* debhelper-compat 12
* debian/control: Added
python3-htseq, rna-star, picard-tools, gmap, histat2, subread, kallisto,
- r-bioc-{edger,deseq2,rots,ctc,biobase,qvalue,goseq,tximport},
- r-cran-{ape,fastcluster,gplots}, and liburi-perl deps
+ r-bioc-{edger,deseq2,rots,ctc,biobase,qvalue,goseq,tximport,dexseq,glimma},
+ r-cran-{ape,fastcluster,gplots,argparse,goplot,readr,tidyverse},
+ liburi-perl deps, and python3-hisat2
* Standards-Version: 4.5.0 (routine-update)
* Refresh patches
* Add salsa-ci file (routine-update)
@@ -14,8 +15,15 @@ trinityrnaseq (2.10.0+dfsg-1) UNRELEASED; urgency=medium
* Use secure URI in Homepage field.
* debian/rules: seqtk-trinity now has a unversioned path
* debian/patches/butterfly: restore missing Butterfly sources
+ * debian/patches/submake: use $(MAKE) consistently
* Install the new bamsfilter plugin
- * TODO: package r-bioc-{glimma,tximportData} and r-cran-{argparse,goplot}
+ * Install trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl
+ * Install trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py
+ * Install PyLib/Pipeliner.py
+ * Set PICARD_HOME default of /usr/share/java
+ * Skip tests that require GATK4 until it gets packaged
+ * Skip tests that require r-bioc-tximportdata
+ * Skip the remaining tests waiting for new packages
-- Michael R. Crusoe <michael.crusoe at gmail.com> Sun, 26 Apr 2020 17:01:55 +0200
=====================================
debian/control
=====================================
@@ -25,6 +25,7 @@ Build-Depends: debhelper-compat (= 12),
r-cran-ape,
r-bioc-ctc,
r-cran-gplots,
+ r-cran-readr,
r-bioc-biobase,
r-bioc-qvalue,
r-bioc-goseq,
@@ -35,7 +36,13 @@ Build-Depends: debhelper-compat (= 12),
gmap,
hisat2,
subread,
- kallisto
+ kallisto,
+ python3-hisat2
+# r-cran-argparse,
+# r-cran-goplot,
+# r-bioc-dexseq,
+# r-bioc-glimma,
+# r-bioc-tximportdata
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/trinityrnaseq
Vcs-Git: https://salsa.debian.org/med-team/trinityrnaseq.git
@@ -67,6 +74,7 @@ Depends: ${shlibs:Depends},
python3-numpy,
ncbi-blast+,
python3,
+ r-cran-readr,
r-bioc-edger,
r-bioc-deseq2,
r-bioc-rots,
@@ -84,12 +92,18 @@ Depends: ${shlibs:Depends},
gmap,
hisat2,
subread,
- kallisto
+ kallisto,
+ python3-hisat2
+# r-cran-argparse,
+# r-cran-goplot,
+# r-bioc-dexseq,
+# r-bioc-glimma
Recommends: ${java:Recommends},
trinityrnaseq-examples,
- tidyverse,
+ r-cran-tidyverse,
picard-tools
-Suggests: collectl
+Suggests: collectl,
+ r-bioc-tximportdata
Description: RNA-Seq De novo Assembly
Trinity represents a novel method for the efficient and robust de novo
reconstruction of transcriptomes from RNA-seq data. Trinity combines three
=====================================
debian/patches/fix_system_paths
=====================================
@@ -2761,3 +2761,14 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print "$cmd\n";
}
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
++++ trinityrnaseq/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
+@@ -143,7 +143,7 @@
+
+ args = parser.parse_args()
+
+- PICARD_HOME = os.getenv("PICARD_HOME")
++ PICARD_HOME = os.getenv("PICARD_HOME", "/usr/share/java")
+ if not PICARD_HOME:
+ exit("Error, missing path to Picard-Tools in $PICARD_HOME.")
+
=====================================
debian/patches/series
=====================================
@@ -12,3 +12,9 @@ python3
unfix_num_of_cores
hardening
seqtk-trinity-hardening
+skip_gatk_test
+skip_tximportData_tests
+submake
+skip_r-cran-argpase
+skip_r-bioc-dexseq
+skip_blat
=====================================
debian/patches/skip_blat
=====================================
@@ -0,0 +1,14 @@
+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 \
+ test_SuperTranscript \
+ test_TPM_weighted_gene_length \
+-test_ExN50 \
+-test_Assembly_DiffReadFormattings
++test_ExN50
+
+
+ test:
=====================================
debian/patches/skip_gatk_test
=====================================
@@ -0,0 +1,12 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: Skip tests that require GATK4 until it gets packaged
+--- trinityrnaseq.orig/trinity_ext_sample_data/Makefile
++++ trinityrnaseq/trinity_ext_sample_data/Makefile
+@@ -8,7 +8,6 @@
+ test_profiling_report \
+ test_PtR \
+ test_DTU \
+-test_VariantCalling \
+ test_tximport \
+ test_SuperTranscript \
+ test_GOplot \
=====================================
debian/patches/skip_r-bioc-dexseq
=====================================
@@ -0,0 +1,12 @@
+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
=====================================
@@ -0,0 +1,21 @@
+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
=====================================
debian/patches/skip_tximportData_tests
=====================================
@@ -0,0 +1,12 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: r-bioc-tximportdata is 400MiB+ package
+--- trinityrnaseq.orig/trinity_ext_sample_data/Makefile
++++ trinityrnaseq/trinity_ext_sample_data/Makefile
+@@ -8,7 +8,6 @@
+ test_profiling_report \
+ test_PtR \
+ test_DTU \
+-test_tximport \
+ test_SuperTranscript \
+ test_GOplot \
+ test_TPM_weighted_gene_length \
=====================================
debian/patches/submake
=====================================
@@ -0,0 +1,166 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Enable better use of sub-make
+--- trinityrnaseq.orig/Inchworm/Makefile
++++ trinityrnaseq/Inchworm/Makefile
+@@ -1,8 +1,8 @@
+ all:
+ mkdir -p build
+- cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install
++ cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && $(MAKE) DESTDIR=../ install
+
+ clean:
+ @echo cleaning
+- (cd build && make clean) || :
++ (cd build && $(MAKE) clean) || :
+ rm -rf ./build ./bin
+--- trinityrnaseq.orig/Makefile
++++ trinityrnaseq/Makefile
+@@ -57,19 +57,19 @@
+
+
+ test_trinity:
+- cd sample_data/test_Trinity_Assembly && make test
++ cd sample_data/test_Trinity_Assembly && $(MAKE) test
+
+
+ # note 'test_all': ** this is for a more advanced installation including devel features **
+
+ test_all:
+- cd sample_data/ && make test_all
++ cd sample_data/ && $(MAKE) test_all
+ ./__pull_trinity_ext_sample_data.sh
+- cd trinity_ext_sample_data/ && make test
++ cd trinity_ext_sample_data/ && $(MAKE) test
+
+ test_clean:
+- cd sample_data/ && make clean
+- cd trinity_ext_sample_data/ && make clean
++ cd sample_data/ && $(MAKE) clean
++ cd trinity_ext_sample_data/ && $(MAKE) clean
+
+ ###################################################################
+
+--- trinityrnaseq.orig/sample_data/Makefile
++++ trinityrnaseq/sample_data/Makefile
+@@ -3,7 +3,7 @@
+ test_all: test_trin_assembly
+
+ test_trin_assembly:
+- cd test_Trinity_Assembly && make test_all
++ cd test_Trinity_Assembly && $(MAKE) test_all
+
+
+ clean:
+--- trinityrnaseq.orig/trinity-plugins/Makefile
++++ trinityrnaseq/trinity-plugins/Makefile
+@@ -26,11 +26,11 @@
+
+
+ htslib.ok:
+- cd htslib && autoreconf && ./configure --prefix=`pwd` && make && make install
++ cd htslib && autoreconf && ./configure --prefix=`pwd` && $(MAKE) && $(MAKE) install
+ @touch htslib.ok
+
+ bamsifter_target: htslib.ok
+- cd bamsifter && make && cp bamsifter ../BIN/
++ cd bamsifter && $(MAKE) && cp bamsifter ../BIN/
+
+ ##################################
+ ### Needed for downstream analyses
+@@ -53,8 +53,8 @@
+ rm -f ./Trimmomatic # rm symlink
+ cd slclust && $(MAKE) clean
+ cd COLLECTL && rm -rf ${COLLECTL_CODE} && rm -f collectl
+- cd htslib && make clean
+- cd bamsifter && make clean
++ cd htslib && $(MAKE) clean
++ cd bamsifter && $(MAKE) clean
+ rm -f ./htslib.ok
+ @echo "\n\n** Done cleaning plugins area **"
+
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_SuperTranscript/Makefile
++++ trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/Makefile
+@@ -1,9 +1,9 @@
+ test:
+ ./runMe.sh
+- cd indiv_tests && make test
++ cd indiv_tests && $(MAKE) test
+ @touch test
+
+ clean:
+ ./cleanMe.sh
+- cd indiv_tests && make clean
++ cd indiv_tests && $(MAKE) clean
+
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
++++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
+@@ -1 +1,2 @@
+-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/10M/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/drosoph_denovo.samples.txt
++MAKE=${MAKE:-make}
++${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/10M/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/drosoph_denovo.samples.txt
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
++++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
+@@ -1 +1,2 @@
+-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/Annotations/Drosoph_coding.cdna SAMPLES=misc_tests/drosoph_ref.samples.txt
++MAKE=${MAKE:-make}
++${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/Annotations/Drosoph_coding.cdna SAMPLES=misc_tests/drosoph_ref.samples.txt
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
++++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
+@@ -1 +1,2 @@
+-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/MOUSE_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/mouse_denovo.samples.txt
++MAKE=${MAKE:-make}
++${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/MOUSE_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/mouse_denovo.samples.txt
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
++++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
+@@ -1 +1,2 @@
+-make TRINITY_FASTA=/seq/regev_genome_portal/RESOURCES/mouse/mm9/Annotations/mm9_ucsc_genomeStudio_genes/mm9_ucsc_genomeStudio_genes.gtf.trans.fa SAMPLES=misc_tests/mouse_ref.samples.txt
++MAKE=${MAKE:-make}
++${MAKE} TRINITY_FASTA=/seq/regev_genome_portal/RESOURCES/mouse/mm9/Annotations/mm9_ucsc_genomeStudio_genes/mm9_ucsc_genomeStudio_genes.gtf.trans.fa SAMPLES=misc_tests/mouse_ref.samples.txt
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
++++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
+@@ -1 +1,2 @@
+-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/SCHIZO_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel_trinity/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/schizo_denovo.samples.txt
++MAKE=${MAKE:-make}
++${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/SCHIZO_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel_trinity/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/schizo_denovo.samples.txt
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
++++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
+@@ -1 +1,2 @@
+-make TRINITY_FASTA=/home/unix/bhaas/utilities/schizo/SP2_GeneDB.290110.prot_coding.cds.nr SAMPLES=misc_tests/schizo_ref.samples.txt
++MAKE=${MAKE:-make}
++${MAKE} TRINITY_FASTA=/home/unix/bhaas/utilities/schizo/SP2_GeneDB.290110.prot_coding.cds.nr SAMPLES=misc_tests/schizo_ref.samples.txt
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
++++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
+@@ -1 +1,2 @@
+-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/10M/trinity_out_dir/Trinity.fasta SAMPLES=drosoph.samples.txt
++MAKE=${MAKE:-make}
++${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/10M/trinity_out_dir/Trinity.fasta SAMPLES=drosoph.samples.txt
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
++++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
+@@ -1 +1,2 @@
+-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/Annotations/Drosoph_coding.cdna SAMPLES=misc_tests/drosoph_ref.samples.txt
++MAKE=${MAKE:-make}
++${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/Annotations/Drosoph_coding.cdna SAMPLES=misc_tests/drosoph_ref.samples.txt
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
++++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
+@@ -1 +1,2 @@
+-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/MOUSE_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel/trinity_out_dir/Trinity.fasta SAMPLES=mouse.samples.txt
++MAKE=${MAKE:-make}
++${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/MOUSE_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel/trinity_out_dir/Trinity.fasta SAMPLES=mouse.samples.txt
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
++++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
+@@ -1 +1,2 @@
+-make TRINITY_FASTA=/seq/regev_genome_portal/RESOURCES/mouse/mm9/Annotations/mm9_ucsc_genomeStudio_genes/mm9_ucsc_genomeStudio_genes.gtf.trans.fa SAMPLES=misc_tests/mouse_ref.samples.txt
++MAKE=${MAKE:-make}
++${MAKE} TRINITY_FASTA=/seq/regev_genome_portal/RESOURCES/mouse/mm9/Annotations/mm9_ucsc_genomeStudio_genes/mm9_ucsc_genomeStudio_genes.gtf.trans.fa SAMPLES=misc_tests/mouse_ref.samples.txt
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
++++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
+@@ -1 +1,2 @@
+-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/SCHIZO_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel_trinity/trinity_out_dir/Trinity.fasta SAMPLES=schizo.samples.txt
++MAKE=${MAKE:-make}
++${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/SCHIZO_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel_trinity/trinity_out_dir/Trinity.fasta SAMPLES=schizo.samples.txt
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
++++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
+@@ -1 +1,2 @@
+-make TRINITY_FASTA=/home/unix/bhaas/utilities/schizo/SP2_GeneDB.290110.prot_coding.cds.nr SAMPLES=misc_tests/schizo_ref.samples.txt
++MAKE=${MAKE:-make}
++${MAKE} TRINITY_FASTA=/home/unix/bhaas/utilities/schizo/SP2_GeneDB.290110.prot_coding.cds.nr SAMPLES=misc_tests/schizo_ref.samples.txt
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-tests
-Depends: @, @builddeps@
+Depends: @, @builddeps@, r-cran-tidyverse
Restrictions: allow-stderr
=====================================
debian/tests/run-tests
=====================================
@@ -15,6 +15,6 @@ rm -f trinityrnaseq/sample_data
cp -rs /usr/share/trinityrnaseq/sample_data trinityrnaseq/
cp -rs /usr/share/trinityrnaseq/trinity_ext_sample_data trinityrnaseq/
cd trinityrnaseq/sample_data
-make test_all
+LD_PRELOAD= make test_all
cd ../trinity_ext_sample_data
LD_PRELOAD= make test
=====================================
debian/trinityrnaseq.install
=====================================
@@ -9,3 +9,6 @@ Trinity /usr/lib/trinityrnaseq
PerlLib /usr/lib/trinityrnaseq/
util /usr/lib/trinityrnaseq/
trinity-plugins/bamsifter/bamsifter /usr/lib/trinityrnaseq/trinity-plugins/BIN/
+trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl /usr/lib/trinityrnaseq/trinity-plugins/COLLECTL/
+trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py /usr/lib/trinityrnaseq/trinity-plugins/DEXseq_util/
+PyLib/Pipeliner.py /usr/lib/trinityrnaseq/PyLib/
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa
--
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa
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