[med-svn] [trinityrnaseq] 02/02: Remove remaining lintian overrides
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu Sep 17 01:06:36 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository trinityrnaseq.
commit c4f099dab78041db4ae6045982c68be392c965e1
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
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 <ahmed at users.sf.net>
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 <crusoe at ucdavis.edu>
+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/*
--
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