Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 56:ee807645b224 draft

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Uploaded
author davidvanzessen
date Mon, 17 Jul 2017 10:44:40 -0400
parents 6cd12c71c3d3
children cb779a45537b
comparison
equal deleted inserted replaced
55:6cd12c71c3d3 56:ee807645b224
39 elif [[ "$type" == *"XZ compressed data"* ]] ; then 39 elif [[ "$type" == *"XZ compressed data"* ]] ; then
40 echo "ZX archive" 40 echo "ZX archive"
41 echo "tar -xJf $input -C $PWD/files/" 41 echo "tar -xJf $input -C $PWD/files/"
42 mkdir -p "$PWD/files/$title" 42 mkdir -p "$PWD/files/$title"
43 tar -xJf $input -C "$PWD/files/$title" 43 tar -xJf $input -C "$PWD/files/$title"
44 else
45 echo "Unrecognized format $type"
46 echo "Unrecognized format $type" > $log
47 exit 1
44 fi 48 fi
45 49
46 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt 50 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
47 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt 51 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
48 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt 52 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt
50 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt 54 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
51 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt 55 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
52 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt 56 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
53 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt 57 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
54 58
59 echo "---------------- unique id check ----------------"
60
61 Rscript $dir/check_unique_id.r $PWD/summary.txt $PWD/sequences.txt $PWD/gapped_aa.txt $PWD/aa.txt $PWD/junction.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt
62
55 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then 63 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
56 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}" 64 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
57 else 65 else
58 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin" 66 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
59 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}" 67 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
67 echo "---------------- merge_and_filter.r ----------------" 75 echo "---------------- merge_and_filter.r ----------------"
68 echo "---------------- merge_and_filter.r ----------------<br />" >> $log 76 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
69 77
70 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1 78 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1
71 79
72 if [[ "$fast" == "no" ]] ; then 80 if [[ "${naive_output}" == "yes" ]] ; then
73 81
74 echo "---------------- creating new IMGT zips ----------------" 82 echo "---------------- creating new IMGT zips ----------------"
75 echo "---------------- creating new IMGT zips ----------------<br />" >> $log 83 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
76 84
77 mkdir $outdir/new_IMGT 85 mkdir $outdir/new_IMGT