# HG changeset patch
# User ulfschaefer
# Date 1467988484 14400
# Node ID 2e0e0e1963862d2691d9a15ce02c66b3a9ad8dba
# Parent 4adc881442c373d1ba6eecb20d75efd072b50809
Deleted selected files
diff -r 4adc881442c3 -r 2e0e0e196386 tool_data_table_conf.xml.sample
--- a/ tool_data_table_conf.xml.sample Fri Jul 08 10:31:11 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-
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- value, dbkey, name, time_stamp, file_path
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diff -r 4adc881442c3 -r 2e0e0e196386 MOST.sh
--- a/MOST.sh Fri Jul 08 10:31:11 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-#!/bin/bash
-
-echo $@
-
-FWDFILE=$1
-shift
-REVFILE=$1
-shift
-OUTXML=$1
-shift
-OUTCSV=$1
-shift
-ORGANISM=$1
-
-OUTFOLDER=$(mktemp -d --tmpdir tmpMOST_XXXXXXXXXXXXXXXXXXXX)
-rm -rf $OUTFOLDER # MOST insists on creating the folder itself
-
-CMD="MOST.py -1 $FWDFILE -2 $REVFILE -o $OUTFOLDER -st $ORGANISM"
-
-echo $CMD
-eval $CMD
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-STEM=$(basename $FWDFILE)
-STEM="${STEM%.*}"
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-mv $OUTFOLDER"/"$STEM"_MLST_result.csv" $OUTCSV
-mv "$OUTFOLDER/$STEM.results.xml" $OUTXML
-
-rm -rf $OUTFOLDER
diff -r 4adc881442c3 -r 2e0e0e196386 MOST.xml
--- a/MOST.xml Fri Jul 08 10:31:11 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-
- Determine MLST from sequencing reads
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- python
- lxml
- pyyaml
- numpy
- biopython
- bowtie2
- samtools
- emboss
- blast_plus
- phemost
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- MOST.sh
- $fwd_file
- $rev_file
- $out1
- $out2
- "${organism.fields.file_path}"
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- https://github.com/phe-bioinformatics/MOST
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diff -r 4adc881442c3 -r 2e0e0e196386 tool_dependencies.xml
--- a/tool_dependencies.xml Fri Jul 08 10:31:11 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
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