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Binary file deseq-hts_1.0/._setup_deseq-hts.sh has changed
--- a/deseq-hts_1.0/README Wed May 09 20:43:47 2012 -0400
+++ b/deseq-hts_1.0/README Wed Jun 27 15:35:11 2012 -0400
@@ -1,5 +1,5 @@
---------------------------------------------------
-DESeq-hts: A Galaxy wrapper for DESeq version 1.6.0
+DESeq-hts: A Galaxy wrapper for DESeq version 1.6.1
---------------------------------------------------
Description:
Binary file deseq-hts_1.0/bin/._deseq_config.sh has changed
Binary file deseq-hts_1.0/bin/._genarglist.sh has changed
Binary file deseq-hts_1.0/bin/._genes_cell2struct has changed
Binary file deseq-hts_1.0/bin/._get_read_counts has changed
Binary file deseq-hts_1.0/bin/._start_interpreter.sh has changed
Binary file deseq-hts_1.0/galaxy/._deseq.xml has changed
--- a/deseq-hts_1.0/galaxy/deseq.xml Wed May 09 20:43:47 2012 -0400
+++ b/deseq-hts_1.0/galaxy/deseq.xml Wed Jun 27 15:35:11 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="deseq-hts" name="DESeq" version="1.6.0">
+<tool id="deseq-hts" name="DESeq" version="1.6.1">
<description>Determines differentially expressed transcripts from read alignments</description>
<command>
deseq-hts/src/deseq-hts.sh $anno_input_selected $deseq_out $deseq_out.extra_files_path/gene_map.mat
@@ -6,6 +6,7 @@
#for $j in $i.replicates
$j.bam_alignment:#slurp
#end for
+
#end for
>> $Log_File </command>
<inputs>
Binary file deseq-hts_1.0/mex/._Makefile has changed
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Binary file deseq-hts_1.0/mex/._get_reads_direct.cpp has changed
Binary file deseq-hts_1.0/mex/._get_reads_direct.h has changed
Binary file deseq-hts_1.0/mex/._interval_overlap.cpp has changed
Binary file deseq-hts_1.0/mex/._mex_input.cpp has changed
Binary file deseq-hts_1.0/mex/._mex_input.h has changed
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Binary file deseq-hts_1.0/mex/._read.h has changed
Binary file deseq-hts_1.0/src/._deseq-hts.sh has changed
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Binary file deseq-hts_1.0/src/._difftest_deseq.R has changed
Binary file deseq-hts_1.0/src/._genes_cell2struct.m has changed
Binary file deseq-hts_1.0/src/._get_read_counts.m has changed
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Binary file deseq-hts_1.0/src/._remove_reads_from_other_genes.m has changed
--- a/deseq-hts_1.0/src/deseq-hts.sh Wed May 09 20:43:47 2012 -0400
+++ b/deseq-hts_1.0/src/deseq-hts.sh Wed Jun 27 15:35:11 2012 -0400
@@ -68,7 +68,7 @@
tmpfile=`mktemp --tmpdir=/tmp`
echo "${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile $@"
-${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile $@ 2>&1
+${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile "$@" 2>&1
echo
echo %%%%%%%%%%%%%%%%%%%%%%%%%%%
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Binary file deseq-hts_1.0/test_data/._deseq_c_elegans_WS200-I-regions-SRX001875.bam.bai has changed
Binary file deseq-hts_1.0/test_data/._deseq_c_elegans_WS200-I-regions.gff3 has changed
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Binary file deseq-hts_1.0/tools/._ParseGFF.py has changed
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Binary file deseq-hts_1.0/tools/._separate.m has changed
--- a/deseq-hts_1.0/tools/ParseGFF.py Wed May 09 20:43:47 2012 -0400
+++ b/deseq-hts_1.0/tools/ParseGFF.py Wed Jun 27 15:35:11 2012 -0400
@@ -342,7 +342,7 @@
def __main__():
"""This function provides a best way to extract genome feature
- information from a GFF3 file for the rQuant downstream processing.
+ information from a GFF3 file for the downstream processing.
"""
try:
gff_file = sys.argv[1]
