[med-svn] [trinityrnaseq] 01/04: drop extra files, ship more docs

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository trinityrnaseq.

commit 32e052f4f7846611639b36ca933c34b20c2efd27
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Fri Jan 29 13:26:21 2016 -0800

    drop extra files, ship more docs
---
 debian/copyright          |  5 +++++
 debian/patches/hashbang   | 33 +--------------------------------
 debian/trinityrnaseq.docs |  2 ++
 3 files changed, 8 insertions(+), 32 deletions(-)

diff --git a/debian/copyright b/debian/copyright
index 40ed223..178778d 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -18,6 +18,11 @@ Files-Excluded: trinity-plugins/jellyfish-*.tar.gz
  galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml~
  Analysis/GenomeViewPlugin/*
  Chrysalis/MakeDepend.dSYM/*
+ util/R/noiseq.r
+ util/deprecated
+ sample_data/test_DE_analysis/deprecated
+ hpc_conf/deprecated
+ Analysis/DifferentialExpression/deprecated
 
 Files: *
 Copyright: © 2011 The Broad Institute, Inc
diff --git a/debian/patches/hashbang b/debian/patches/hashbang
index 1a0eb2b..b4dceab 100644
--- a/debian/patches/hashbang
+++ b/debian/patches/hashbang
@@ -40,35 +40,4 @@ Description: add #! lines as needed
 @@ -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_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/run_DESeq2.sh
-+++ trinityrnaseq/sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/run_DESeq2.sh
-@@ -1 +1,3 @@
-+#! /bin/sh
-+
- ../../../Analysis/DifferentialExpression/run_DE_analysis.pl --matrix counts.matrix --samples_file samples.txt --method DESeq2
---- trinityrnaseq.orig/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/cleanMe.sh
-+++ trinityrnaseq/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/cleanMe.sh
-@@ -1,2 +1,4 @@
-+#! /bin/sh
-+
- rm -rf ./edgeR.*.dir
- 
---- trinityrnaseq.orig/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/runMe.sh
-+++ trinityrnaseq/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/runMe.sh
-@@ -1 +1,3 @@
-+#! /bin/sh
-+
- ../../../Analysis/DifferentialExpression/run_DE_analysis.pl --matrix example.matrix --method edgeR
---- trinityrnaseq.orig/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/cleanMe.sh
-+++ trinityrnaseq/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/cleanMe.sh
-@@ -1 +1,3 @@
-+#! /bin/sh
-+
- rm -f MA_plot.eps  diff_expr.results.txt
---- trinityrnaseq.orig/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/runMe.sh
-+++ trinityrnaseq/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/runMe.sh
-@@ -1 +1,3 @@
-+#! /bin/sh
-+
- R --vanilla -q < run_edgeR_on_sample_data.R 
+
diff --git a/debian/trinityrnaseq.docs b/debian/trinityrnaseq.docs
index 4b272eb..837d1fc 100644
--- a/debian/trinityrnaseq.docs
+++ b/debian/trinityrnaseq.docs
@@ -1,3 +1,5 @@
 README
 Release.Notes
 debian/tests/run-tests
+galaxy-plugin
+hpc_conf

-- 
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