compatibility change for lncRNA-screen

code/By_Sample

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ -f code/custom_bash_profile ]; then source code/custom_bash_profile; fi # shell settings
+source code/custom-bashrc
 
 CWD=`pwd`
 
@@ -11,6 +11,10 @@ fi
 params=$1
 SAMPLE=$2
 
+
+if [ `cat $CWD/${SAMPLE}.out | wc -l` -eq 1 ]; then exec >> $CWD/$SAMPLE.out;else exec > $CWD/$SAMPLE.out; fi
+exec 2>&1
+
 FLAG=0
 if [ ! -z `qstat -j $JOB_ID | grep "tmp_free" | sed 's/ +//g' | cut -d ' ' -f1` ]
 then

code/Summarize

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ -f code/custom_bash_profile ]; then source code/custom_bash_profile; fi # shell settings
+source code/custom-bashrc
 
 if [ "$#" -ne 4 ] && [ "$#" -ne 3 ]
 then
@@ -20,6 +20,9 @@ group_sheet=`basename $group_info | sed 's/\.txt$//g'`
 
 params=`cat $PARAMS | grep "^DESeq2" | cut -f2`
 
+if [ `cat ${GROUP}.out | wc -l` -eq 1 ]; then exec >> $GROUP.out;else exec > $GROUP.out; fi
+exec 2>&1
+
 cd $OUT_DIR
 
 mkdir -p $group_sheet

code/align_summary

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ -f code/custom_bash_profile ]; then source code/custom_bash_profile; fi # shell settings
+source code/custom-bashrc
 
 if [ "$#" -lt 1 ]; then
         printf "\n\n###### Usage\n\n"

code/custom-bashrc

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+
+PS1="[\u@\h \W]\$ "
+
+
+PATH=code/:code/bin/:code/utilities/:code/utilities/STAR/:code/utilities/sratoolkit/:code/utilities/cufflinks/:code/utilities/CPAT/:code/utilities/fastqc/:code/utilities/subread:$PATH
+
+PYTHONPATH=code/utilities/utilities/CPAT/lib/:$PYTHONPATH
+
+export LC_ALL=C
+export PATH
+export PYTHONPATH
+
+export PERL5LIB=$HOME/lib
+export EDITOR="/usr/local/bin/mate -w"
+
+module load samtools/0.1.19
+module load r/3.3.0
+module load python/2.7

code/generate_STAR-Index

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ -f code/custom_bash_profile ]; then source code/custom_bash_profile; fi # shell settings
+source code/custom-bashrc
 
 if [ "$#" -lt 2 ]; then
         printf "\n\n###### Usage\n\n"

code/generate_rnaseq_tracks

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ -f code/custom_bash_profile ]; then source code/custom_bash_profile; fi # shell settings
+source code/custom-bashrc
 
 if [ "$#" -ne 4 ]; then
         printf "\n\n###### Usage\n\n"

code/gtf_id2name

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ -f code/custom_bash_profile ]; then source code/custom_bash_profile; fi # shell settings
+source code/custom-bashrc
 
 if [ "$#" -ne 1 ]; then
         printf "\n\n###### Usage\n\n"
@@ -12,10 +12,12 @@ INP=$1
 TEMP1=$(mktemp)
 TEMP2=$(mktemp)
 
-cat $1 | awk '$3~/exon/'| perl -F/\\t/ -lane '@des=split(/ \"|\";\s{0,1}/,$F[8]);for($i=0;$i<@des;$i=$i+2){if($des[$i]=~/gene_id/){$gene_id=$des[$i+1]}elsif($des[$i]=~/gene_name/){$gene_name=$des[$i+1]}else{}}print "$gene_name\t$gene_id"' | sort | uniq | mergeuniq -merge > $TEMP1
+cat $INP | grep -v "^#" | awk '{if($1!~/^chr/){print "chr"$0}else{print $0}}' | awk '$3~/exon/'| perl -F/\\t/ -lane '@des=split(/ \"|\";\s{0,1}/,$F[8]);for($i=0;$i<@des;$i=$i+2){if($des[$i]=~/gene_id/){$gene_id=$des[$i+1]}elsif($des[$i]=~/gene_name/){$gene_name=$des[$i+1]}else{}}print "$gene_name\t$gene_id"' | sort | uniq | mergeuniq -merge > $TEMP1
 
 cat $TEMP1 | grep " " | key-expand | cols -t 1 0 | awk '{print $1"\t"$1":"$2}' > $TEMP2 
 
 cat $TEMP1 | grep -v " " | cols -t 1 0 >> $TEMP2
 
 cat $TEMP2 | sort -k1,1 | mergeuniq -merge | tr ' ' '|' > ${INP%.*}.id2name.txt
+
+rm -rf $TEMP1 $TEMP2

code/job_submitter.bash

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+source code/custom-bashrc
+
+NSLOTS=$1
+shift
+
+qsub -b Y -cwd -pe threaded $NSLOTS -l tmp_free=120G -l tmp_token=30G -hard $@

code/run_alignment

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ -f code/custom_bash_profile ]; then source code/custom_bash_profile; fi # shell settings
+source code/custom-bashrc
 
 
 if [ "$#" -ne 5 ] && [ "$#" -ne 4 ] && [ "$#" -ne 3 ]

code/run_assembly

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ -f code/custom_bash_profile ]; then source code/custom_bash_profile; fi # shell settings
+source code/custom-bashrc
 
 if [ "$#" -lt 3 ]; then
         printf "\n\n###### Usage\n\n"

code/run_fastq-download

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ -f code/custom_bash_profile ]; then source code/custom_bash_profile; fi # shell settings
+source code/custom-bashrc
 
 
 if [ "$#" -lt 2 ]; then
@@ -87,9 +87,9 @@ then
 cd $OUT_DIR/$name_sample/
 
 printf "\n\n***** Downloading $id_sample/${id_file} into $OUT_DIR/$name_sample Using fastq-dump.2...\n"
-echo "../code/utilities/sratoolkit/fastq-dump.2 --tries 10 --split-files -A "$id_file" -gzip" >> run.bash
+echo "../code/utilities/sratoolkit/fastq-dump.2.4.2 --tries 10 --split-files -A "$id_file" -gzip" >> run.bash
 pwd
-../code/utilities/sratoolkit/fastq-dump.2 --tries 10 --split-files -A $id_file -gzip
+../code/utilities/sratoolkit/fastq-dump.2.4.2 --tries 10 --split-files -A $id_file -gzip
 
 cd $CWD
 		done

code/run_fastq-link

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ -f code/custom_bash_profile ]; then source code/custom_bash_profile; fi # shell settings
+source code/custom-bashrc
 
 if [ "$#" -lt 3 ]; then
 	printf "\n\n###### Usage\n\n"

code/run_fastqc

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ -f code/custom_bash_profile ]; then source code/custom_bash_profile; fi # shell settings
+source code/custom-bashrc
 
 if [ "$#" -lt 2 ]; then
         printf "\n\n###### Usage\n\n"

code/setup_waiting.bash

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+source code/custom-bashrc
+
+INPUT=$@
+
+for element in ${INPUT[@]}
+do
+	echo "###### START ######" > ${element}.out
+done

code/summarize_raw_count

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ -f code/custom_bash_profile ]; then source code/custom_bash_profile; fi # shell settings
+source code/custom-bashrc
 
 TEMP="$#"
 FILE_COUNT=$((TEMP*2))

code/utilities/CPAT

@@ -0,0 +1 @@
+CPAT-1.2.2/

code/utilities/CPAT-1.2.2/MANIFEST.in

@@ -0,0 +1,53 @@
+include distribute_setup.py
+recursive-include src *.h
+recursive-include src *.c
+recursive-include lib *.h
+recursive-include lib *.c
+recursive-include lib *.pyx
+recursive-include doc *
+
+#include MANIFEST.in
+#include KNOWN_BUGS
+#include ez_setup.py
+include dat/*
+include test/*
+include lib/pysam/csamtools.pxd
+include lib/pysam/csamtools.pyx
+include lib/pysam/csamtools.c
+include lib/pysam/ctabix.pxd
+include lib/pysam/ctabix.c
+include lib/pysam/ctabix.pyx
+include lib/pysam/TabProxies.c
+include lib/pysam/TabProxies.pyx
+include lib/pysam/TabProxies.pxd
+include lib/pysam/cvcf.pyx
+include lib/pysam/cvcf.pxd
+include lib/pysam/cvcf.c
+include lib/pysam/pysam_util.h
+include lib/samtools/*.h
+include lib/samtools/*/*.h
+include lib/tabix/*.h
+
+# pysam tests
+include lib/tests/00README.txt
+include lib/tests/Makefile
+include lib/tests/ex1.fa
+include lib/tests/ex1.sam.gz
+include lib/tests/ex3.sam
+include lib/tests/ex4.sam
+include lib/tests/ex5.sam
+include lib/tests/ex6.sam
+include lib/tests/ex7.sam
+include lib/tests/ex8.sam
+include lib/tests/ex9_fail.bam
+include lib/tests/ex9_nofail.bam
+include lib/tests/ex10.sam
+include lib/tests/example.py
+include lib/tests/pysam_test.py
+include lib/tests/segfault_tests.py
+
+# tabix tests
+include lib/tests/tabix_test.py
+include lib/tests/example.gtf.gz
+include lib/tests/example.gtf.gz.tbi
+

code/utilities/CPAT-1.2.2/PKG-INFO

@@ -0,0 +1,11 @@
+Metadata-Version: 1.0
+Name: CPAT
+Version: 1.2.2
+Summary: Coding Potential Assessment Tool
+Home-page: http://rna-cpat.sourceforge.net/
+Author: Liguo Wang
+Author-email: [email protected]
+License: UNKNOWN
+Description: UNKNOWN
+Platform: Linux
+Platform: MacOS