# HG changeset patch
# User iuc
# Date 1479467200 18000
# Node ID ac47ba06cd57e2b52336cf8fcc633bc7ac3fd159
# Parent  0b06ab8d5f887afeb35622a5204fcd7830286544
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd

diff -r 0b06ab8d5f88 -r ac47ba06cd57 run_de_analysis.xml
--- a/run_de_analysis.xml	Mon Aug 01 11:52:05 2016 -0400
+++ b/run_de_analysis.xml	Fri Nov 18 06:06:40 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.0">
+<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.1">
     <description>using a Trinity assembly</description>
     <macros>
         <import>macros.xml</import>
@@ -159,6 +159,8 @@
 ConditionC  CondC_replicate3
 =========== ================
 
+
+This file can be generated with the 'Describe samples and replicates' tool.
 It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification'.
 The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'.
 
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/express_bowtie/results.xprs.genes
--- a/test-data/count/express_bowtie/results.xprs.genes	Mon Aug 01 11:52:05 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-bundle_id	target_id	length	eff_length	tot_counts	uniq_counts	est_counts	eff_counts	ambig_distr_alpha	ambig_distr_beta	fpkm	fpkm_conf_low	fpkm_conf_high	solvable	tpm
-NA	TRINITY_DN3_c0_g1	216.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
-NA	TRINITY_DN2_c2_g1	240.00	240.00	NA	NA	NA	1.00	NA	NA	378787.90	NA	NA	NA	60178.11
-NA	TRINITY_DN2_c3_g1	202.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
-NA	TRINITY_DN0_c0_g1	229.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
-NA	TRINITY_DN2_c0_g1	279.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
-NA	TRINITY_DN1_c0_g1	380.00	109.25	NA	NA	NA	17.39	NA	NA	4160711.00	NA	NA	NA	661013.1
-NA	TRINITY_DN2_c1_g1	541.00	259.01	NA	NA	NA	10.44	NA	NA	1754947.00	NA	NA	NA	278808.8
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/express_bowtie/results_B.xprs.genes
--- a/test-data/count/express_bowtie/results_B.xprs.genes	Mon Aug 01 11:52:05 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-bundle_id	target_id	length	eff_length	tot_counts	uniq_counts	est_counts	eff_counts	ambig_distr_alpha	ambig_distr_beta	fpkm	fpkm_conf_low	fpkm_conf_high	solvable	tpm
-NA	TRINITY_DN3_c0_g1	216.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
-NA	TRINITY_DN2_c1_g1	240.00	240.00	NA	NA	NA	1.00	NA	NA	378787.90	NA	NA	NA	60178.11
-NA	TRINITY_DN2_c3_g1	202.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
-NA	TRINITY_DN0_c0_g1	380.00	109.25	NA	NA	NA	17.39	NA	NA	4160711.00	NA	NA	NA	661013.1
-NA	TRINITY_DN1_c0_g1	229.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
-NA	TRINITY_DN2_c0_g1	279.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
-NA	TRINITY_DN2_c2_g1	541.00	259.01	NA	NA	NA	10.44	NA	NA	1754947.00	NA	NA	NA	278808.8
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/express_bowtie/sample_A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/sample_A	Fri Nov 18 06:06:40 2016 -0500
@@ -0,0 +1,8 @@
+bundle_id	target_id	length	eff_length	tot_counts	uniq_counts	est_counts	eff_counts	ambig_distr_alpha	ambig_distr_beta	fpkm	fpkm_conf_low	fpkm_conf_high	solvable	tpm
+NA	TRINITY_DN3_c0_g1	216.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c2_g1	240.00	240.00	NA	NA	NA	1.00	NA	NA	378787.90	NA	NA	NA	60178.11
+NA	TRINITY_DN2_c3_g1	202.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN0_c0_g1	229.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c0_g1	279.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN1_c0_g1	380.00	109.25	NA	NA	NA	17.39	NA	NA	4160711.00	NA	NA	NA	661013.1
+NA	TRINITY_DN2_c1_g1	541.00	259.01	NA	NA	NA	10.44	NA	NA	1754947.00	NA	NA	NA	278808.8
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/express_bowtie/sample_B
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/sample_B	Fri Nov 18 06:06:40 2016 -0500
@@ -0,0 +1,8 @@
+bundle_id	target_id	length	eff_length	tot_counts	uniq_counts	est_counts	eff_counts	ambig_distr_alpha	ambig_distr_beta	fpkm	fpkm_conf_low	fpkm_conf_high	solvable	tpm
+NA	TRINITY_DN3_c0_g1	216.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c1_g1	240.00	240.00	NA	NA	NA	1.00	NA	NA	378787.90	NA	NA	NA	60178.11
+NA	TRINITY_DN2_c3_g1	202.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN0_c0_g1	380.00	109.25	NA	NA	NA	17.39	NA	NA	4160711.00	NA	NA	NA	661013.1
+NA	TRINITY_DN1_c0_g1	229.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c0_g1	279.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c2_g1	541.00	259.01	NA	NA	NA	10.44	NA	NA	1754947.00	NA	NA	NA	278808.8
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/rsem_bowtie/RSEM.genes.results
--- a/test-data/count/rsem_bowtie/RSEM.genes.results	Mon Aug 01 11:52:05 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
-TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	229.00	11.55	0.00	0.00	0.00
-TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	380.00	123.91	5.00	329523.81	3668378.58
-TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	35.45	0.00	0.00	0.00
-TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	541.00	281.27	5.00	145165.14	1616031.03
-TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	240.00	15.55	1.00	525311.05	5847953.22
-TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.45	0.00	0.00	0.00
-TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.82	0.00	0.00	0.00
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/rsem_bowtie/RSEM.genes_B.results
--- a/test-data/count/rsem_bowtie/RSEM.genes_B.results	Mon Aug 01 11:52:05 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
-TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	229.00	11.55	0.00	0.00	0.00
-TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	380.00	123.91	5.00	329523.81	3668378.58
-TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	35.45	0.00	0.00	0.00
-TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	541.00	281.27	5.00	145165.14	1616031.03
-TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	240.00	15.55	1.00	525311.05	5847953.22
-TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.45	0.00	0.00	0.00
-TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.82	0.00	0.00	0.00
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/rsem_bowtie/sample_A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/sample_A	Fri Nov 18 06:06:40 2016 -0500
@@ -0,0 +1,8 @@
+gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	229.00	11.55	0.00	0.00	0.00
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	380.00	123.91	5.00	329523.81	3668378.58
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	35.45	0.00	0.00	0.00
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	541.00	281.27	5.00	145165.14	1616031.03
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	240.00	15.55	1.00	525311.05	5847953.22
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.45	0.00	0.00	0.00
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.82	0.00	0.00	0.00
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/rsem_bowtie/sample_B
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/sample_B	Fri Nov 18 06:06:40 2016 -0500
@@ -0,0 +1,8 @@
+gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	229.00	11.55	0.00	0.00	0.00
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	380.00	123.91	5.00	329523.81	3668378.58
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	35.45	0.00	0.00	0.00
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	541.00	281.27	5.00	145165.14	1616031.03
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	240.00	15.55	1.00	525311.05	5847953.22
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.45	0.00	0.00	0.00
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.82	0.00	0.00	0.00
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/rsem_bowtie2/RSEM.genes.results
--- a/test-data/count/rsem_bowtie2/RSEM.genes.results	Mon Aug 01 11:52:05 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
-TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	229.00	10.58	0.00	0.00	0.00
-TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	380.00	122.00	5.00	309046.31	3415300.55
-TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	32.50	0.00	0.00	0.00
-TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	541.00	279.67	6.00	161779.66	1787842.67
-TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	240.00	14.25	1.00	529174.03	5847953.22
-TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.17	0.00	0.00	0.00
-TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.25	0.00	0.00	0.00
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/rsem_bowtie2/RSEM.genes_B.results
--- a/test-data/count/rsem_bowtie2/RSEM.genes_B.results	Mon Aug 01 11:52:05 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
-TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	380.00	122.00	5.00	309046.31	3415300.55
-TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	229.00	10.58	0.00	0.00	0.00
-TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	32.50	0.00	0.00	0.00
-TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	541.00	279.67	6.00	161779.66	1787842.67
-TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	240.00	14.25	1.00	529174.03	5847953.22
-TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.17	0.00	0.00	0.00
-TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.25	0.00	0.00	0.00
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/rsem_bowtie2/sample_A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/sample_A	Fri Nov 18 06:06:40 2016 -0500
@@ -0,0 +1,8 @@
+gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	229.00	10.58	0.00	0.00	0.00
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	380.00	122.00	5.00	309046.31	3415300.55
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	32.50	0.00	0.00	0.00
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	541.00	279.67	6.00	161779.66	1787842.67
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	240.00	14.25	1.00	529174.03	5847953.22
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.17	0.00	0.00	0.00
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.25	0.00	0.00	0.00
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/rsem_bowtie2/sample_B
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/sample_B	Fri Nov 18 06:06:40 2016 -0500
@@ -0,0 +1,8 @@
+gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	380.00	122.00	5.00	309046.31	3415300.55
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	229.00	10.58	0.00	0.00	0.00
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	32.50	0.00	0.00	0.00
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	541.00	279.67	6.00	161779.66	1787842.67
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	240.00	14.25	1.00	529174.03	5847953.22
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.17	0.00	0.00	0.00
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.25	0.00	0.00	0.00
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/salmon/quant.sf
--- a/test-data/count/salmon/quant.sf	Mon Aug 01 11:52:05 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-Name	Length	EffectiveLength	TPM	NumReads
-TRINITY_DN1_c0_g1_i1	380	120.403	179183	13
-TRINITY_DN0_c0_g1_i1	229	229	55271.5	7.62686
-TRINITY_DN2_c0_g1_i1	279	31.1522	565494	10.6151
-TRINITY_DN2_c1_g1_i1	541	278.129	113370	19
-TRINITY_DN2_c2_g1_i1	240	240	32900.7	4.75801
-TRINITY_DN2_c3_g1_i1	202	202	0	0
-TRINITY_DN3_c0_g1_i1	216	216	53781.8	7
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/salmon/quant.sf.genes
--- a/test-data/count/salmon/quant.sf.genes	Mon Aug 01 11:52:05 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-Name	Length	EffectiveLength	TPM	NumReads
-TRINITY_DN2_c2_g1	240.00	240.00	32900.70	4.76
-TRINITY_DN0_c0_g1	229.00	229.00	55271.50	7.63
-TRINITY_DN1_c0_g1	380.00	120.40	179183.00	13.00
-TRINITY_DN2_c0_g1	279.00	31.15	565494.00	10.62
-TRINITY_DN2_c3_g1	202.00	202.00	0.00	0.00
-TRINITY_DN3_c0_g1	216.00	216.00	53781.80	7.00
-TRINITY_DN2_c1_g1	541.00	278.13	113370.00	19.00
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/salmon/sample_A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/sample_A	Fri Nov 18 06:06:40 2016 -0500
@@ -0,0 +1,8 @@
+Name	Length	EffectiveLength	TPM	NumReads
+TRINITY_DN1_c0_g1_i1	380	120.403	179183	13
+TRINITY_DN0_c0_g1_i1	229	229	55271.5	7.62686
+TRINITY_DN2_c0_g1_i1	279	31.1522	565494	10.6151
+TRINITY_DN2_c1_g1_i1	541	278.129	113370	19
+TRINITY_DN2_c2_g1_i1	240	240	32900.7	4.75801
+TRINITY_DN2_c3_g1_i1	202	202	0	0
+TRINITY_DN3_c0_g1_i1	216	216	53781.8	7
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/count/salmon/sample_B
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/sample_B	Fri Nov 18 06:06:40 2016 -0500
@@ -0,0 +1,8 @@
+Name	Length	EffectiveLength	TPM	NumReads
+TRINITY_DN2_c2_g1	240.00	240.00	32900.70	4.76
+TRINITY_DN0_c0_g1	229.00	229.00	55271.50	7.63
+TRINITY_DN1_c0_g1	380.00	120.40	179183.00	13.00
+TRINITY_DN2_c0_g1	279.00	31.15	565494.00	10.62
+TRINITY_DN2_c3_g1	202.00	202.00	0.00	0.00
+TRINITY_DN3_c0_g1	216.00	216.00	53781.80	7.00
+TRINITY_DN2_c1_g1	541.00	278.13	113370.00	19.00
diff -r 0b06ab8d5f88 -r ac47ba06cd57 test-data/samples.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples.tsv	Fri Nov 18 06:06:40 2016 -0500
@@ -0,0 +1,4 @@
+ConditionA	CondA_replicate1
+ConditionA	CondA_replicate2
+ConditionB	CondB_replicate1
+ConditionB	CondB_replicate2
diff -r 0b06ab8d5f88 -r ac47ba06cd57 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Aug 01 11:52:05 2016 -0400
+++ b/tool_dependencies.xml	Fri Nov 18 06:06:40 2016 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="trinity" version="2.2.0">
-        <repository changeset_revision="58d411f36881" name="package_trinity_2_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="e7df326a23e6" name="package_trinity_2_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="bowtie" version="1.1.2">
         <repository changeset_revision="8584a4574ab1" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
@@ -9,11 +9,8 @@
     <package name="bowtie2" version="2.2.6">
         <repository changeset_revision="9d2f1e2f5919" name="package_bowtie_2_2_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="samtools" version="1.2">
-        <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
     <package name="bioconductor-edger" version="3.14.0">
-        <repository changeset_revision="d1ebebe12abc" name="package_bioconductor_edger_3_14_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="68b9124afe32" name="package_bioconductor_edger_3_14_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="rsem" version="1.2.28">
         <repository changeset_revision="987ca85aead4" name="package_rsem_1_2_28" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
@@ -22,7 +19,7 @@
         <repository changeset_revision="690e3e7d202b" name="package_express_1_5_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="bioconductor-limma" version="3.28.10">
-        <repository changeset_revision="90b7c39ce562" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="aa9f79cf4640" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="deseq2" version="1.10.0">
        <repository changeset_revision="5d9def29ff0b" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />