cf017baa8d
* chlorop: new package * chlorop: moving main script to bin and moving runtime tmp location. * chlorop: fixing flake8 error. * chlorop: cleaning up, removing CHLOROTMP, advising user to set it. * chlorop: removing unused import
37 lines
1.3 KiB
Diff
37 lines
1.3 KiB
Diff
--- a/chlorop 2006-03-20 06:24:22.000000000 -0600
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+++ b/chlorop 2017-07-24 10:51:27.000366706 -0500
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@@ -9,8 +9,6 @@
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STARTDIR=`pwd`
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### GENERAL SETTINGS, CUSTOMIZE +++++++++++++++++++++++++++++++++++++++++++++++
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-# Substitute your chosen location for ChloroP software:
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-CHLOROP=/usr/cbs/packages/chlorop/currdist/chlorop-1.1
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# Substitute paste:
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PASTE=paste
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@@ -43,7 +41,7 @@
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# other settings:
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#CHLOROTMPNAME=res`date '+%y%m%d%H%M%S'`.$$
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CHLOROTMPNAME=res.$$
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-CHLOROTMP=tmp/$CHLOROTMPNAME
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+CHLOROTMP=$CHLOROTMP/$CHLOROTMPNAME
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SCRIPTS=bin
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SYN=syn
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ETC=etc
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@@ -80,12 +78,12 @@
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### get the infile ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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INFILE=$*
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-mkdir $CHLOROP/$CHLOROTMP || { echo Cannot create temporary directory; exit 1; }
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+mkdir -p $CHLOROTMP || { echo Cannot create temporary directory; exit 1; }
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### prepare input file in HOW and fasta format ++++++++++++++++++++++++++++++++
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$AWK -f $CHLOROP/$SCRIPTS/in2how+fasta.awk -v informat=$INFORMAT \
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- -v howout=$CHLOROP/$CHLOROTMP/infile.how \
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- -v fastaout=$CHLOROP/$CHLOROTMP/infile.fasta $INFILE
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+ -v howout=$CHLOROTMP/infile.how \
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+ -v fastaout=$CHLOROTMP/infile.fasta $INFILE
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INFILE=$CHLOROTMP/infile.how
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### change to working directory +++++++++++++++++++++++++++++++++++++++++++++++
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