# HG changeset patch
# User chrisw
# Date 1549990585 18000
# Node ID ae546ad6f2f45130cbbbc62ac0fb1f0aec0c1a60
# Parent  b08c5567f2f04f21120aabf297742bbe18ae9856
Uploaded

diff -r b08c5567f2f0 -r ae546ad6f2f4 monorail.sh
--- a/monorail.sh	Tue Feb 12 11:21:33 2019 -0500
+++ b/monorail.sh	Tue Feb 12 11:56:25 2019 -0500
@@ -1,12 +1,6 @@
 set -o pipefail -o errexit 
-#get this script's path
-#p=`perl -e '@f=split("/","'$0'"); pop(@f); print "".join("/",@f)."\n";'`
-
-#/data7/miniconda2/envs/_galaxy_18.09/bin:/data7/miniconda2/condabin:/home/cwilks/.nimble/bin:/data/pypy3-v6.0.0-linux64/bin:/home/cwilks/zstd_dir:/data/bedtools2/bin:/usr/local/cuda-8.0/bin:/home/cwilks/Python3/bin:/data2/sqlite-autoconf-3110000.fts5:/data/java/bin:/data/ant/bin:/home/cwilks/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/cwilks/samtools-1.2:/home/cwilks/samtools-1.2/htslib-1.2.1:/data/WiggleTools/bin:/data/kent_tools:/data2/liftover:/home/cwilks/bin
 
 path2=$PATH
-#starp=`/bin/which STAR`
-#stp=`/bin/which samtools`
 
 #e.g. /data7/references/ath10/star_idx
 ref=$1
@@ -23,10 +17,6 @@
 #e.g. tmp/SRR8505407_SRP182756_ath10_sra_2.fastq.gz, just leave off if not paired
 reads2=$7
 
-
-#racc=`perl -e '$r1="'${reads1}'"; @f=split(/\//,$r1); $r1=pop(@f); ($n1)=split(/[\._]/,$r1); print "$n1\n";'`
-
-#cd ${tmp}
 #align
 STAR --runMode alignReads --runThreadN $threads --genomeDir ${ref} --readFilesIn $reads1 $reads2 --readFilesCommand zcat --twopassMode None --outReadsUnmapped Fastx --outMultimapperOrder Random --outSAMreadID Number --readFilesType Fastx --outTmpDir ./star_tmp --outSAMtype BAM Unsorted --outSAMmode NoQS --outSAMattributes NH MD --chimOutType Junctions --chimOutJunctionFormat 1 --chimSegmentReadGapMax 3 --chimJunctionOverhangMin 12 --chimSegmentMin 12 > star.log 2>&1
 
@@ -39,8 +29,4 @@
 samtools index -@ $threads $sorted_bam >> stools.log 2>&1
 
 #get coverage summaries
-#bamcount $sorted_bam --threads $threads --coverage --no-head --require-mdz --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --annotation $annotation bc --auc bc --lats bc > bc.log 2>&1 
-
-#echo $PATH > ${sorted_bam}.bai
-#echo $starp >> ${sorted_bam}.bai
-#echo $stp >> ${sorted_bam}.bai
+bamcount $sorted_bam --threads $threads --coverage --no-head --require-mdz --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --annotation $annotation bc --auc bc --lats bc > bc.log 2>&1