#!/bin/bash
PATH=/mnt/raid/tools/align/bowtie2/bowtie2-2.1.0:/mnt/raid/tools/align/tophat-2.0.9.Linux_x86_64:/home/reczko/.opam/system/bin:/data/results/tools/align/blast/ncbi-blast-2.2.29+/bin:/home/reczko/a/tools/rna/structural-motifs/CMfinder_0.2/bin:/home/reczko/a/tools/libs/www/firefox:/home/reczko/a/tools/libs/boost/bin:/data/results/tools/ml/torch/torch/install/bin:/data/results/tools/chipseq/ngsplot/bin:/data/results/tools/bedtools/BEDTools-Version-2.14.3/bin:/data/results/tools/samtools/mysamtools-0.1.19:/data/results/tools/denovo/gene-finding/snap:/data/results/tools/denovo/gene-finding/exonerate-2.2.0-x86_64/bin:/data/results/tools/denovo/gene-finding/augustus-3.0.3/bin:/data/results/tools/denovo/gene-finding/augustus-3.0.3/scripts:/data/results/tools/align/blast/ncbi-blast-2.2.29+/bin:/data/results/tools/denovo/repeats/RepeatMasker:/data/results/tools/protein/tmhmm-2.0c/bin:/data/results/tools/align/rsem/rsem-1.2.15:/data/results/tools/chipseq/ngsplot/bin:/home/reczko/a/tools/libs/java/jdk1.8.0_66/bin:/home/reczko/a/tools/ml/tensorflow/bazel/output:/usr/lib/jvm/java-7-openjdk-amd64/jre/bin:/usr/java/jre1.8.0_45/bin:/data/results/tools/samtools/samtools-1.0:/data/results/tools/align/bowtie-1.1.0:/data/results/tools/r/R-3.0.1/bin:/data/results/tools/ml/torch/torch/install/bin:/home/reczko/bin:/home/reczko/.opam/system/bin:/data/results/tools/align/blast/ncbi-blast-2.2.29+/bin:/home/reczko/a/tools/rna/structural-motifs/CMfinder_0.2/bin:/home/reczko/a/tools/libs/www/firefox:/home/reczko/a/tools/libs/boost/bin:/data/results/tools/ml/torch/torch/install/bin:/data/results/tools/chipseq/ngsplot/bin:/data/results/tools/bedtools/BEDTools-Version-2.14.3/bin:/data/results/tools/samtools/mysamtools-0.1.19:/data/results/tools/denovo/gene-finding/snap:/data/results/tools/denovo/gene-finding/exonerate-2.2.0-x86_64/bin:/data/results/tools/denovo/gene-finding/augustus-3.0.3/bin:/data/results/tools/denovo/gene-finding/augustus-3.0.3/scripts:/data/results/tools/align/blast/ncbi-blast-2.2.29+/bin:/data/results/tools/denovo/repeats/RepeatMasker:/data/results/tools/protein/tmhmm-2.0c/bin:/data/results/tools/align/rsem/rsem-1.2.15:/data/results/tools/chipseq/ngsplot/bin:/home/reczko/a/tools/libs/java/jdk1.8.0_66/bin:/home/reczko/a/tools/ml/tensorflow/bazel/output:/usr/lib/jvm/java-7-openjdk-amd64/jre/bin:/usr/java/jre1.8.0_45/bin:/data/results/tools/samtools/samtools-1.0:/data/results/tools/align/bowtie-1.1.0:/data/results/tools/r/R-3.0.1/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/data/results/tools/rna/protein-coding-potential/lncRScan-SVM_v1.0.1/executable/script:/data/results/tools/rna/protein-coding-potential/lncRScan-SVM_v1.0.1/executable/util:/data/results/tools/rna/protein-coding-potential/lncRScan-SVM_v1.0.1/executable/bin/x86_64:/data/results/tools/rna/protein-coding-potential/lncRScan-SVM_v1.0.1/executable/script:/data/results/tools/rna/protein-coding-potential/lncRScan-SVM_v1.0.1/executable/util:/data/results/tools/rna/protein-coding-potential/lncRScan-SVM_v1.0.1/executable/bin/x86_64; export PATH
echo "Using bowtie installation at"
which bowtie2
bowtie2 --version
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.KLPNC1-ecoli-res.IonXpress_017.fastq |samtools view -Sb - > 2.bam 2> 02_.bowtie2-mm9.log
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.KLPNC2-Trs502.IonXpress_018.fastq |samtools view -Sb - > 2.bam 2> 02_.bowtie2-mm9.log
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.KLPNC3-Trs8.IonXpress_019.fastq |samtools view -Sb - > 2.bam 2> 02_.bowtie2-mm9.log
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC51-ChIRP-Input.IonXpress_020.fastq |samtools view -Sb - > 2.bam 2> 02_.bowtie2-mm9.log
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC52-ChIRP-ODD.IonXpress_021.fastq |samtools view -Sb - > 2.bam 2> 02_.bowtie2-mm9.log
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC53-ChIRP-EVEN.IonXpress_022.fastq |samtools view -Sb - > 2.bam 2> 02_.bowtie2-mm9.log
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC54-ChIRP-LacZ.IonXpress_023.fastq |samtools view -Sb - > 2.bam 2> 02_.bowtie2-mm9.log
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC55-MCF-Input.IonXpress_024.fastq |samtools view -Sb - > 2.bam 2> 02_.bowtie2-mm9.log
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC56-MCF-Acl2.IonXpress_025.fastq |samtools view -Sb - > 2.bam 2> 02_.bowtie2-mm9.log
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC57-MCF-bcat.IonXpress_026.fastq |samtools view -Sb - > 2.bam 2> 02_.bowtie2-mm9.log
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC58-MCF-TCF4.IonXpress_027.fastq |samtools view -Sb - > 2.bam 2> 02_.bowtie2-mm9.log
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.YAbR24-OD3-C3719-3.IonXpress_005.fastq |samtools view -Sb - > 2.bam 2> 02_.bowtie2-mm9.log