Mercurial > repos > iuc > trinity

changeset 12:ceacea4ee49e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
author iuc
date Fri, 18 Nov 2016 06:07:04 -0500
parents 80c6d1ec9cd7
children 0105dd727713
files test-data/count/express_bowtie/results.xprs.genes test-data/count/express_bowtie/results_B.xprs.genes test-data/count/express_bowtie/sample_A test-data/count/express_bowtie/sample_B test-data/count/rsem_bowtie/RSEM.genes.results test-data/count/rsem_bowtie/RSEM.genes_B.results test-data/count/rsem_bowtie/sample_A test-data/count/rsem_bowtie/sample_B test-data/count/rsem_bowtie2/RSEM.genes.results test-data/count/rsem_bowtie2/RSEM.genes_B.results test-data/count/rsem_bowtie2/sample_A test-data/count/rsem_bowtie2/sample_B test-data/count/salmon/quant.sf test-data/count/salmon/quant.sf.genes test-data/count/salmon/sample_A test-data/count/salmon/sample_B test-data/samples.tsv tool_dependencies.xml trinity.xml
diffstat 19 files changed, 71 insertions(+), 71 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/count/express_bowtie/results.xprs.genes	Wed Jul 27 08:42:10 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
--- a/test-data/count/express_bowtie/results_B.xprs.genes	Wed Jul 27 08:42:10 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/sample_A	Fri Nov 18 06:07:04 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/sample_B	Fri Nov 18 06:07:04 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
--- a/test-data/count/rsem_bowtie/RSEM.genes.results	Wed Jul 27 08:42:10 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
--- a/test-data/count/rsem_bowtie/RSEM.genes_B.results	Wed Jul 27 08:42:10 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/sample_A	Fri Nov 18 06:07:04 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/sample_B	Fri Nov 18 06:07:04 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
--- a/test-data/count/rsem_bowtie2/RSEM.genes.results	Wed Jul 27 08:42:10 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
--- a/test-data/count/rsem_bowtie2/RSEM.genes_B.results	Wed Jul 27 08:42:10 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/sample_A	Fri Nov 18 06:07:04 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/sample_B	Fri Nov 18 06:07:04 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
--- a/test-data/count/salmon/quant.sf	Wed Jul 27 08:42:10 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
--- a/test-data/count/salmon/quant.sf.genes	Wed Jul 27 08:42:10 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/sample_A	Fri Nov 18 06:07:04 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/sample_B	Fri Nov 18 06:07:04 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples.tsv	Fri Nov 18 06:07:04 2016 -0500
@@ -0,0 +1,4 @@
+ConditionA	CondA_replicate1
+ConditionA	CondA_replicate2
+ConditionB	CondB_replicate1
+ConditionB	CondB_replicate2
--- a/tool_dependencies.xml	Wed Jul 27 08:42:10 2016 -0400
+++ b/tool_dependencies.xml	Fri Nov 18 06:07:04 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" />
--- a/trinity.xml	Wed Jul 27 08:42:10 2016 -0400
+++ b/trinity.xml	Fri Nov 18 06:07:04 2016 -0500
@@ -5,7 +5,6 @@
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="1.1.2">bowtie</requirement>
-        <requirement type="package" version="1.2">samtools</requirement>
         <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement>
     </expand>
     <expand macro="stdio"/>