| Previous changeset 0:8922a3be8490 (2018-06-04) |
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Commit message:
Uploaded |
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added:
export_info.xml manifest.xml star_icgc_alignment2-8922a3be8490.tar.gz |
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removed:
star_alignment/.shed.yml star_alignment/ICGC_pipeline.sh star_alignment/ICGC_pipeline_RUN.sh star_alignment/STAR star_alignment/icgc_star2_wrapper.xml star_alignment/star_align.py |
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| diff -r 8922a3be8490 -r b566013f81e8 export_info.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/export_info.xml Tue Jul 24 03:38:01 2018 -0400 |
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| @@ -0,0 +1,11 @@ +<?xml version="1.0"?> +<export_info> + <export_time>Tue, 24 Jul 2018 07:36:35 +0000</export_time> + <tool_shed>https://toolshed.g2.bx.psu.edu</tool_shed> + <repository_name>star_icgc_alignment2</repository_name> + <repository_owner>daumsoft</repository_owner> + <changeset_revision>8922a3be8490</changeset_revision> + <export_repository_dependencies>False</export_repository_dependencies> + <exported_via_api>False</exported_via_api> +</export_info> + |
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| diff -r 8922a3be8490 -r b566013f81e8 manifest.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/manifest.xml Tue Jul 24 03:38:01 2018 -0400 |
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| @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<repositories> + <repository name="star_icgc_alignment2" type="unrestricted" username="daumsoft"> + <description>star_icgc_alignment of daumsoft</description> + <long_description>star_icgc_alignment of daumsoft</long_description> + <archive>star_icgc_alignment2-8922a3be8490.tar.gz</archive> + <categories> + <category>Transcriptomics</category> + </categories> + </repository> +</repositories> + |
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| diff -r 8922a3be8490 -r b566013f81e8 star_alignment/.shed.yml --- a/star_alignment/.shed.yml Mon Jun 04 02:38:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -categories: [Transcriptomics] -description: daumsoft -name: tar -owner: daumsoft -remote_repository_url: https://toolshed.g2.bx.psu.edu/view/daumsoft |
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| diff -r 8922a3be8490 -r b566013f81e8 star_alignment/ICGC_pipeline.sh --- a/star_alignment/ICGC_pipeline.sh Mon Jun 04 02:38:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,51 +0,0 @@ -#!/bin/bash - -if [ "$#" -ne 1 ]; then - echo "[usage:] ICGC_pipeline.sh fastq_in_tar.gz" - exit 1; -fi - -#FASTQ_1=$1 -#FASTQ_2=$2 -#SAMPLE_ID=$3 -#TAR_FILE=$SAMPLE_ID".tar" -TAR_FILE=$1 - -export PATH=/storage/data/program/GDC_TGCA-Harmonized/RNA-Seq/bin/ICGC-STAR_ALIGNMENT_PIPELINE:$PATH - -#tar cvfh $TAR_FILE $FASTQ_2 $FASTQ_1 - -STAD_ALIGN=~/package/DAUMSOFT/RNA-seq/ICGC_STAR_ALIGNMENT_PIPELINE/star_align.py -STAR_INDEX_PATH=~/refs/hg38/gdc/Index_Files/GDC.h38.d1.vd1_STAR2_Index_Files/star_genome_d1_vd1_gtfv22 -WORK_DIR=./wrk -OUTPUT_BAM=./out -REFERENCE=~/refs/hg38/gdc/GRCh38.d1.vd1_Reference_Sequence/GRCh38.d1.vd1.fa -RUN_THREAD_NUM=8 -rm -rf $WORK_DIR -rm -rf $OUTPUT_BAM -mkdir $WORK_DIR -mkdir $OUTPUT_BAM - -python $STAD_ALIGN \ ---genomeDir $STAR_INDEX_PATH \ ---tarFileIn $TAR_FILE \ ---workDir $WORK_DIR \ ---out $OUTPUT_BAM \ ---genomeFastaFiles $REFERENCE \ ---runThreadN $RUN_THREAD_NUM \ ---outFilterMultimapScoreRange 1 \ ---outFilterMultimapNmax 20 \ ---outFilterMismatchNmax 10 \ ---alignIntronMax 500000 \ ---alignMatesGapMax 1000000 \ ---sjdbScore 2 \ ---limitBAMsortRAM 0 \ ---alignSJDBoverhangMin 1 \ ---genomeLoad NoSharedMemory \ ---outFilterMatchNminOverLread 0.33 \ ---outFilterScoreMinOverLread 0.33 \ ---twopass1readsN -1 \ ---sjdbOverhang 100 \ ---outSAMstrandField intronMotif \ ---outSAMunmapped Within - |
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| diff -r 8922a3be8490 -r b566013f81e8 star_alignment/ICGC_pipeline_RUN.sh --- a/star_alignment/ICGC_pipeline_RUN.sh Mon Jun 04 02:38:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,14 +0,0 @@ -#!/bin/bash - -if [ "$#" -ne 1 ]; then - echo "[usage:] ICGC_pipeline_RUN.sh tar.gz(fastq in file)" - exit 1; -fi - -INPUT_TAR_GZ=$1 - -ln -s $INPUT_TAR_GZ ${INPUT_TAR_GZ}.tar.gz -INPUT_TAR_GZ=${INPUT_TAR_GZ}.tar.gz - -$GALAXY_HOME/package/DAUMSOFT/RNA-seq/ICGC_STAR_ALIGNMENT_PIPELINE/ICGC_pipeline.sh $INPUT_TAR_GZ > log.out 2>&1 - |
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| diff -r 8922a3be8490 -r b566013f81e8 star_alignment/STAR |
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| Binary file star_alignment/STAR has changed |
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| diff -r 8922a3be8490 -r b566013f81e8 star_alignment/icgc_star2_wrapper.xml --- a/star_alignment/icgc_star2_wrapper.xml Mon Jun 04 02:38:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,36 +0,0 @@ -<tool id="daumsoft_wts_star" name="ICGC_STAR_PIPELINE" version="2.4.2A"> - <description>STAR Alignment/ICGC Method</description> - <stdio> - <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/> - </stdio> - <version_command></version_command> - <command> - - \$GALAXY_HOME/package/DAUMSOFT/RNA-seq/ICGC_STAR_ALIGNMENT_PIPELINE/ICGC_pipeline_RUN.sh - ${tar_gz} - - </command> - <inputs> - <param name="tar_gz" format="gz" type="data" label="RNA-Seq FASTQ file In TAR.GZ(GRCh38)/hg38" help="" /> - </inputs> - <outputs> - <data format="bam" name="alignment" label="${tool.name} on ${on_string}: Alignments BAM" from_work_dir="out/Aligned.sortedByCoord.out.bam"/> - </outputs> - <tests><test><output name="alignment"/></test></tests> - <help> - -For more detailed manual, please visit The GDC mRNA quantification analysis pipeline website: - -https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline - -The mRNA Analysis pipeline begins with the Alignment Workflow, which is performed using a two-pass method with STAR. -STAR aligns each read group separately and then merges the resulting alignments into one. -Following the methods used by the International Cancer Genome Consortium ICGC, -the two-pass method includes a splice junction detection step, which is used to generate the final alignment. - -This workflow outputs a BAM file, which contains both aligned and unaligned reads. -Quality assessment is performed pre-alignment with FASTQC and post-alignment with RNA-SeQC and Picard Tools. - - </help> - <citations></citations> -</tool> |
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| diff -r 8922a3be8490 -r b566013f81e8 star_alignment/star_align.py --- a/star_alignment/star_align.py Mon Jun 04 02:38:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,527 +0,0 @@\n-#!/usr/bin/env python\n-\n-import os\n-import sys\n-import re\n-import string\n-import tempfile\n-import subprocess\n-import argparse\n-import shutil\n-import lxml.etree as etree\n-import fnmatch\n-\n-def walk_dir(base, pattern):\n- files = []\n- for root, dirnames, filenames in os.walk(base):\n- for fname in fnmatch.filter(filenames, pattern):\n- files.append(os.path.join(root, fname))\n- return files\n-\n-def scan_workdir(base): \n-\n- ### scan for paired-end files\n- #############################\n-\n- ### unzipped fastq input\n- fastq_files = walk_dir(base, "*_read[12]_*fastq")\n- if len(fastq_files):\n- o = {}\n- for i in sorted(fastq_files):\n- basename = re.sub(r\'_read[12]\', \'\', i)\n- try:\n- o[basename].append(i)\n- except KeyError:\n- o[basename] = [i]\n- if not all( (len(i) == 2 for i in o.values())):\n- raise Exception("Missing Pair")\n- return ( \'cat\', list( (os.path.basename(i), o[i][0], o[i][1]) for i in o.keys()), \'PE\') \n-\n- ### unzipped fastq input\n- fastq_files = walk_dir(base, "*_R[12]_001.fastq")\n- if len(fastq_files):\n- o = {}\n- for i in fastq_files:\n- basename = re.sub(r\'_R[12]_001.fastq$\', \'\', i)\n- o[basename] = o.get(basename, 0) + 1\n- if not all( (i == 2 for i in o.values())):\n- raise Exception("Missing Pair")\n- return ( \'cat\', list( (os.path.basename(i), "%s_R1_001.fastq" % i,"%s_R2_001.fastq" % i) for i in o.keys()), \'PE\') \n-\n- ### unzipped fastq input\n- fastq_files = walk_dir(base, "*_[12].fastq")\n- if len(fastq_files):\n- o = {}\n- for i in fastq_files:\n- basename = re.sub(r\'_[12].fastq$\', \'\', i)\n- o[basename] = o.get(basename, 0) + 1\n- if not all( (i == 2 for i in o.values())):\n- raise Exception("Missing Pair")\n- return ( \'cat\', list( (os.path.basename(i), "%s_1.fastq" % i,"%s_2.fastq" % i) for i in o.keys()), \'PE\') \n-\n- ### unzipped fastq input\n- fastq_files = walk_dir(base, "*[.][12].fastq")\n- if len(fastq_files):\n- o = {}\n- for i in fastq_files:\n- basename = re.sub(r\'[.][12].fastq$\', \'\', i)\n- o[basename] = o.get(basename, 0) + 1\n- if not all( (i == 2 for i in o.values())):\n- raise Exception("Missing Pair")\n- return ( \'cat\', list( (os.path.basename(i), "%s.1.fastq" % i,"%s.2.fastq" % i) for i in o.keys()), \'PE\') \n-\n- ### unzipped fastq input\n- fastq_files = walk_dir(base, "*.fastq[12]")\n- if len(fastq_files):\n- o = {}\n- for i in fastq_files:\n- basename = re.sub(r\'.fastq[12]$\', \'\', i)\n- o[basename] = o.get(basename, 0) + 1\n- if not all( (i == 2 for i in o.values())):\n- raise Exception("Missing Pair")\n- return ( \'cat\', list( (os.path.basename(i), "%s.fastq1" % i,"%s.fastq2" % i) for i in o.keys()), \'PE\') \n-\n- ### unzipped txt input\n- fastq_files = walk_dir(base, "*_[12]_sequence.txt")\n- if len(fastq_files):\n- o = {}\n- for i in fastq_files:\n- basename = re.sub(r\'_[12]_sequence.txt$\', \'\', i)\n- o[basename] = o.get(basename, 0) + 1\n- if not all( (i == 2 for i in o.values())):\n- raise Exception("Missing Pair")\n- return ( \'cat\', list( (os.path.basename(i), "%s_1_sequence.txt" % i,"%s_2_sequence.txt" % i) for i in o.keys()), \'PE\') \n- \n- ### gzipped input\n- fastq_gz_files = walk_dir(base, "*_[12].fastq.gz")\n- if len(fastq_gz_files):\n- o = {}\n- for i in fastq_gz_files:\n- basename = re.sub(r\'_[12].fastq.gz$\', \'\', i)\n- o[basename] = o.get(basename, 0) + 1\n- if not all( (i == 2 for i in o.values())):\n- raise Exception("Missing Pair")\n- return ( \'zcat\', list( (os.path.basename(i), "%s_1.fastq.gz" % i,"%s_2.fastq.gz" % i) for i in o.keys()), \'PE\') \n-\n- ### bzipped input\n-'..b'lign_template_str).safe_substitute({\n- \'genomeDir\' : genome_dir,\n- \'runThreadN\' : args.runThreadN,\n- \'fastq_left\' : \',\'.join([os.path.join(x[0], x[1]) for x in align_sets[1]]), #os.path.abspath(pair[1]),\n- \'outFilterMultimapScoreRange\' : args.outFilterMultimapScoreRange,\n- \'outFilterMultimapNmax\' : args.outFilterMultimapNmax,\n- \'outFilterMismatchNmax\' : args.outFilterMismatchNmax,\n- \'alignIntronMax\' : args.alignIntronMax,\n- \'alignMatesGapMax\': args.alignMatesGapMax,\n- \'sjdbScore\': args.sjdbScore,\n- \'alignSJDBoverhangMin\' : args.alignSJDBoverhangMin,\n- \'genomeLoad\' : args.genomeLoad,\n- \'limitBAMsortRAM\' : args.limitBAMsortRAM,\n- \'readFilesCommand\' : align_sets[0],\n- \'outFilterMatchNminOverLread\' : args.outFilterMatchNminOverLread,\n- \'outFilterScoreMinOverLread\' : args.outFilterScoreMinOverLread,\n- \'sjdbOverhang\' : args.sjdbOverhang,\n- \'outSAMstrandField\' : args.outSAMstrandField,\n- \'outSAMattributes\' : " ".join(args.outSAMattributes),\n- \'outSAMunmapped\' : args.outSAMunmapped, \n- \'outSAMtype\' : " ".join(args.outSAMtype),\n- \'outSAMheaderHD\' : " ".join(args.outSAMheaderHD)\n- })\n-# \'twopass1readsN\' : args.twopass1readsN,\n- if align_sets[2] == \'PE\':\n- cmd = string.Template(cmd).substitute({\n- \'fastq_right\' : \',\'.join([os.path.join(x[0], x[2]) for x in align_sets[1]]) # os.path.abspath(pair[2]),\n- })\n-\n- ### convert RG_dict into formatted RG line\n- RG_line = []\n- for r, readgroup in enumerate(align_sets[1]):\n- if \'RG\' in RG_dict:\n- tmp = \'ID:%s:%s\' % (RG_dict[\'ID\'], RG_dict[\'RG\'][r])\n- else:\n- tmp = \'ID:%s:%s\' % (RG_dict[\'ID\'], readgroup[0])\n- if len(RG_dict) > 1:\n- tmp += \'\\t\'\n- tmp += \'\\t\'.join([\'%s:%s\' % (key, RG_dict[key]) for key in RG_dict if key not in [\'ID\', \'RG\', \'SI\']])\n- ### add read group label\n- if \'RG\' in RG_dict and \'CN\' in RG_dict:\n- tmp += \'\\tPU:%s:%s\' % (RG_dict[\'CN\'], RG_dict[\'RG\'][r])\n- RG_line.append(\'%s\' % tmp)\n- cmd += \' --outSAMattrRGline %s\' % \' , \'.join(RG_line)\n-\n- ### handle comment lines\n- comment_file = None\n- if \'SI\' in RG_dict:\n- if args.useTMP is not None:\n- comment_file = os.path.abspath( tempfile.mkstemp(dir=os.environ[args.useTMP], prefix="star_comments_")[1] )\n- else:\n- comment_file = os.path.abspath( tempfile.mkstemp(dir=args.workDir, prefix="star_comments_")[1] )\n- \n- fd_com = open(comment_file, \'w\')\n- fd_com.write(\'@CO\\tsubmitter_sample_id:%s\\n\' % RG_dict[\'SI\'])\n-\n- fd_com.flush()\n- fd_com.close()\n- \n- cmd += \' --outSAMheaderCommentFile %s\' % comment_file\n-\n-\n- ### take temp directory from environment variable\n- if args.useTMP is not None:\n- align_dir = os.path.abspath( tempfile.mkdtemp(dir=os.environ[args.useTMP], prefix="star_aligndir_") )\n- else:\n- align_dir = os.path.abspath( tempfile.mkdtemp(dir=args.workDir, prefix="star_aligndir_") )\n- print "Running", cmd\n- subprocess.check_call(cmd, shell=True, cwd=align_dir)\n-\n- ### move output file\n- if \'BAM\' in args.outSAMtype and \'SortedByCoordinate\' in args.outSAMtype:\n- shutil.move(os.path.join(align_dir, \'Aligned.sortedByCoord.out.bam\'), args.out)\n- elif \'BAM\' in args.outSAMtype and \'Unsorted\' in args.outSAMtype:\n- shutil.move(os.path.join(align_dir, \'Aligned.out.bam\'), args.out)\n- else:\n- raise Exception(\'STAR output file could not be determined\') \n-\n- ### move junctions if to be kept\n- if args.keepJunctions:\n- shutil.move(os.path.join(align_dir, \'SJ.out.tab\'), args.out + \'.junctions\')\n-\n- ### clean up working directory\n- shutil.rmtree(workdir)\n- shutil.rmtree(align_dir)\n- if args.twopass1readsN != 0:\n- shutil.rmtree(align_dir_1st)\n- shutil.rmtree(genome_dir_1st)\n' |
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| diff -r 8922a3be8490 -r b566013f81e8 star_icgc_alignment2-8922a3be8490.tar.gz |
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| Binary file star_icgc_alignment2-8922a3be8490.tar.gz has changed |