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commit c4f099dab78041db4ae6045982c68be392c965e1 Author: Michael R. Crusoe <[email protected]> Date: Wed Sep 16 15:16:33 2015 -0700 Remove remaining lintian overrides add #! as needed install sample data to /usr/share & symlink into /usr/lib/ --- debian/copyright | 2 +- debian/patches/hashbang | 81 +++++++++++++++++++++++++ debian/patches/series | 1 + debian/rules | 9 ++- debian/trinityrnaseq-examples.install | 2 +- debian/trinityrnaseq-examples.links | 1 + debian/trinityrnaseq-examples.lintian-overrides | 2 - debian/trinityrnaseq.lintian-overrides | 1 - 8 files changed, 93 insertions(+), 6 deletions(-) diff --git a/debian/copyright b/debian/copyright index 0af1d51..a857477 100644 --- a/debian/copyright +++ b/debian/copyright @@ -26,7 +26,7 @@ Files: Butterfly/src/src/NWalign.java Copyright: Ahmed Moustafa <[email protected]> License: GPL-2+ -Files: trinity-plugins/*Fastool*/kseq.h +Files: trinity-plugins/fstrozzi-Fastool-7c3e034f05/kseq.h Copyright: (c) 2008 Genome Research Ltd (GRL). License: MIT diff --git a/debian/patches/hashbang b/debian/patches/hashbang new file mode 100644 index 0000000..4f606f2 --- /dev/null +++ b/debian/patches/hashbang @@ -0,0 +1,81 @@ +Author: Michael R. Crusoe <[email protected]> +Description: add #! lines as needed +--- trinityrnaseq.orig/sample_data/__regression_tests/test_GraphFromFasta/runMe.sh ++++ trinityrnaseq/sample_data/__regression_tests/test_GraphFromFasta/runMe.sh +@@ -1 +1,2 @@ ++#!/bin/sh + ../../../Chrysalis/GraphFromFasta -i inchworm.K25.L25.fa -r both.fa -min_contig_length 100 -min_glue 0 -glue_factor 0 -min_iso_ratio 0 -t 4 -k 24 -kk 48 +--- trinityrnaseq.orig/sample_data/test_GOSeq_trinotate_pipe/Spombe/runMe.sh ++++ trinityrnaseq/sample_data/test_GOSeq_trinotate_pipe/Spombe/runMe.sh +@@ -1,3 +1,4 @@ ++#!/bin/sh + ../../../Analysis/DifferentialExpression/run_GOseq.pl --factor_labeling hs_induced_vs_log.factors --GO_assignments Trinotate_report.xls.trans.gene_ontology --lengths Trinity.seq_lengths + + ../../../Analysis/DifferentialExpression/run_GOseq.pl --factor_labeling ds_induced_vs_log.factors --GO_assignments Trinotate_report.xls.trans.gene_ontology --lengths Trinity.seq_lengths +--- trinityrnaseq.orig/sample_data/test_Inchworm/runMe_MPI.sh ++++ trinityrnaseq/sample_data/test_Inchworm/runMe_MPI.sh +@@ -1,3 +1,4 @@ ++#!/bin/sh + if [ ! -e jellyfish.kmers.fa ]; then + gunzip -c jellyfish.kmers.fa.gz > jellyfish.kmers.fa + fi +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/align_reads_via_bowtie.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/align_reads_via_bowtie.sh +@@ -1 +1,2 @@ +-/home/unix/bhaas/SVN/trinityrnaseq/trunk/util/bowtie_PE_separate_then_join.pl --seqType fq --left ../reads.left.fq --right ../reads.right.fq --target refSeqs.fa --aligner bowtie -- -p 4 --all --best --strata -m 300 ++#!/bin/bash ++/usr/lib/trinityrnaseq/util/bowtie_PE_separate_then_join.pl --seqType fq --left ../reads.left.fq --right ../reads.right.fq --target refSeqs.fa --aligner bowtie -- -p 4 --all --best --strata -m 300 +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.clean.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.clean.sh +@@ -1 +1,2 @@ ++#!/bin/sh + ../../../../Trinity.pl --seqType fq --left clean.left.fq --right clean.right.fq --seqType fq --JM 1G --bfly_opts "-V 15 --stderr " +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.sh +@@ -1 +1,2 @@ ++#!/bin/sh + ../../../../Trinity.pl --seqType fq --left ex5.reads.left.fq --right ex5.reads.right.fq --seqType fq --JM 1G --bfly_opts "-V 15 --stderr" +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/runMe.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/runMe.sh +@@ -1,2 +1,3 @@ ++#!/bin/sh + ../../Trinity.pl --seqType fq --left ex9.reads.left.fq --right ex9.reads.right.fq --SS_lib_type RF --bfly_opts "--edge-thr=0.05 --stderr -V 18" --run_butterfly --output trinity_outdir + +--- trinityrnaseq.orig/sample_data/test_align_and_estimate_abundance/run_eXpress.sh ++++ trinityrnaseq/sample_data/test_align_and_estimate_abundance/run_eXpress.sh +@@ -1 +1,2 @@ ++#!/bin/sh + ../../util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --gene_trans_map Trinity.fasta.gene_trans_map --aln_method bowtie --est_method eXpress --output_dir eXpress_estimate --SS_lib_type RF +--- trinityrnaseq.orig/sample_data/test_align_and_estimate_abundance/run_rsem.sh ++++ trinityrnaseq/sample_data/test_align_and_estimate_abundance/run_rsem.sh +@@ -1,3 +1,4 @@ ++#!/bin/sh + if [ ! -e Trinity.fasta ]; then + gunzip -c Trinity.fasta.gz > Trinity.fasta + fi +--- trinityrnaseq.orig/sample_data/test_edgeR_diff_expr/example_DESeq2_analysis_pipeline/run_DESeq2.sh ++++ trinityrnaseq/sample_data/test_edgeR_diff_expr/example_DESeq2_analysis_pipeline/run_DESeq2.sh +@@ -1 +1,2 @@ ++#!/bin/sh + ../../../Analysis/DifferentialExpression/run_DE_analysis.pl --matrix counts.matrix --samples_file samples.txt --method DESeq2 +--- trinityrnaseq.orig/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/cleanMe.sh ++++ trinityrnaseq/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/cleanMe.sh +@@ -1,2 +1,3 @@ ++#!/bin/sh + rm -rf ./edgeR.*.dir + +--- trinityrnaseq.orig/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/runMe.sh ++++ trinityrnaseq/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/runMe.sh +@@ -1 +1,2 @@ ++#!/bin/sh + ../../../Analysis/DifferentialExpression/run_DE_analysis.pl --matrix example.matrix --method edgeR +--- trinityrnaseq.orig/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/cleanMe.sh ++++ trinityrnaseq/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/cleanMe.sh +@@ -1 +1,2 @@ ++#!/bin/sh + rm -f MA_plot.eps diff_expr.results.txt +--- trinityrnaseq.orig/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/runMe.sh ++++ trinityrnaseq/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/runMe.sh +@@ -1 +1,2 @@ ++#!/bin/sh + R --vanilla -q < run_edgeR_on_sample_data.R diff --git a/debian/patches/series b/debian/patches/series index e6ba448..4701ce1 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,4 @@ +hashbang chrysalis-make-tweak noExitTester jellyfish-path diff --git a/debian/rules b/debian/rules index 0914720..abcde6e 100755 --- a/debian/rules +++ b/debian/rules @@ -7,6 +7,7 @@ export CLASSPATH=${JDIR}/commons-collections4.jar:${JDIR}/gnu-getopt.jar:${JDIR} export JAVA_HOME=/usr/lib/jvm/default-java SOURCE_DIRECTORIES = Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust BASEDIR=debian/trinityrnaseq/usr/lib/trinityrnaseq +EXBASEDIR=debian/trinityrnaseq-examples/usr/share/trinityrnaseq LAST_CHANGE := $(shell dpkg-parsechangelog -S Date) export BUILD_DATETIME := $(shell LC_ALL=C date -u -d '$(LAST_CHANGE)') @@ -46,7 +47,13 @@ override_dh_install: ${BASEDIR}/Analysis/FL_reconstruction_analysis/count_by_expression_quintile.pl \ ${BASEDIR}/util/misc/capture_orig_n_unmapped_reads.pl \ ${BASEDIR}/util/support_scripts/plugin_install_tests.sh \ - ${BASEDIR}/util/support_scripts/trinity_install_tests.sh + ${BASEDIR}/util/support_scripts/trinity_install_tests.sh \ + ${EXBASEDIR}/sample_data/__regression_tests/test_GraphFromFasta/runMe.sh \ + ${EXBASEDIR}/sample_data/test_Inchworm/runMe_MPI.sh \ + ${EXBASEDIR}/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.clean.sh \ + ${EXBASEDIR}/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.sh + chmod -R a-x ${BASEDIR}/PerlLib/*.pm + chmod -R a-x ${BASEDIR}/PerlLib/*/*.pm get-orig-source: uscan --verbose --force-download --repack --compression xz diff --git a/debian/trinityrnaseq-examples.install b/debian/trinityrnaseq-examples.install index 6c8c1c4..16a5f66 100644 --- a/debian/trinityrnaseq-examples.install +++ b/debian/trinityrnaseq-examples.install @@ -1 +1 @@ -sample_data /usr/lib/trinityrnaseq/ +sample_data /usr/share/trinityrnaseq/ diff --git a/debian/trinityrnaseq-examples.links b/debian/trinityrnaseq-examples.links new file mode 100644 index 0000000..cb49d8c --- /dev/null +++ b/debian/trinityrnaseq-examples.links @@ -0,0 +1 @@ +usr/share/trinityrnaseq/sample_data usr/lib/trinityrnaseq/sample_data diff --git a/debian/trinityrnaseq-examples.lintian-overrides b/debian/trinityrnaseq-examples.lintian-overrides deleted file mode 100644 index 2d13570..0000000 --- a/debian/trinityrnaseq-examples.lintian-overrides +++ /dev/null @@ -1,2 +0,0 @@ -trinityrnaseq-examples: image-file-in-usr-lib usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/* -trinityrnaseq-examples: executable-not-elf-or-script usr/lib/trinityrnaseq/* diff --git a/debian/trinityrnaseq.lintian-overrides b/debian/trinityrnaseq.lintian-overrides deleted file mode 100644 index 19e50fa..0000000 --- a/debian/trinityrnaseq.lintian-overrides +++ /dev/null @@ -1 +0,0 @@ -trinityrnaseq: executable-not-elf-or-script usr/lib/trinityrnaseq/* -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trinityrnaseq.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
