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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,155 @@ | ||
| #!/bin/bash | ||
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| source code/custom-bashrc | ||
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| if [ "$#" -ne 2 ] && [ "$#" -ne 3 ] && [ "$#" -ne 4 ] | ||
| then | ||
| printf "\n###### Usage\n" | ||
| printf "$0 [Optional: Threads (Default 6)] <PARAMS> <OUTPUT_DIR> [Optional: Sample Name] \n" | ||
| exit | ||
| fi | ||
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| date | ||
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| ######################### | ||
| # input | ||
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| if [[ $1 =~ ^[[:digit:]]{1,2}$ ]];then NSLOTS=$1;shift | ||
| elif [[ $NSLOTS == "" ]]; then NSLOTS=6; fi | ||
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| PARAMS=$1 | ||
| OUT_DIR=$2 | ||
| SAMPLE=$3 | ||
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| CWD=`pwd` | ||
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| ######################### | ||
| if [ ! -d $OUT_DIR ]; then mkdir -p $OUT_DIR; fi | ||
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| IFS=$'\n' | ||
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| #header=`cat $PARAMS | grep -E "^#" | head -1 | cut -d' ' -f2` | ||
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| ######################## | ||
| # SRA Download | ||
| for record in `cat $PARAMS | grep -v "^#"` | ||
| do | ||
| name_sample=`echo $record | cut -f1` | ||
| id_sample=`echo $record | cut -f2` | ||
| header=`echo $record | cut -f3` | ||
| if [ "$name_sample" == "$SAMPLE" ] || [ -z "$SAMPLE" ] | ||
| then | ||
| # check for output existance | ||
| if [ ! -d $OUT_DIR/$name_sample ] | ||
| then | ||
| mkdir $OUT_DIR/$name_sample | ||
| fastq_dump_path=`which fastq-dump.2.4.2` | ||
| picard_path=`which picard.jar` | ||
| gdc_client_path=`which gdc-client` | ||
| ### change of directory | ||
| cd $OUT_DIR/$name_sample/ | ||
| echo "#!/bin/bash" > run.bash | ||
| echo "cd $OUT_DIR/$name_sample/ # change of directory" >> run.bash | ||
| else | ||
| echo "Output $OUT_DIR/$name_sample Existing!" | ||
| break | ||
| fi | ||
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| if [ "$header" == "SRA" ]; then | ||
| echo | ||
| echo "###### Downloading $name_sample from $header!" | ||
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| link_sample="ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/${id_sample:0:6}/$id_sample/" | ||
| ID_RUNS=(`curl -sS $link_sample | sed -r 's/\s+/\t/g' | cut -f9 `) | ||
| num_run=0 | ||
| echo "$link_sample" | ||
| mkdir data # creating data directory... | ||
| echo "mkdir data # creating data directory" >> run.bash | ||
| for id_run in "${ID_RUNS[@]}" | ||
| do | ||
| echo " |____ $id_run" | ||
| ((num_run++)) | ||
| num_run=$(printf "%03d" $num_run) | ||
| link_run=${link_sample}${id_run}"/" | ||
| ID_FILES=(`curl -sS $link_run | sed -r 's/\s+/\t/g' | cut -f9 `) | ||
| for name_file in "${ID_FILES[@]}" | ||
| do | ||
| echo " | |____ $id_file" | ||
| echo " | | Retrieving SRA... " | ||
| link_file=${link_run}${name_file} | ||
| wget -nv $link_file # downloading .sra file | ||
| echo "wget -nv $link_file # download .sra file" >> run.bash | ||
| echo " | | Converting SRA..." | ||
| $fastq_dump_path --split-files -gzip $name_file # convert SRA file to fastq.gz file and seperate read1 and read2 | ||
| echo "$fastq_dump_path --split-files -gzip $name_file # convert SRA file to fastq.gz file and seperate read1 and read2" >> run.bash | ||
| id_file=${name_file%.*} | ||
| rm -rf $name_file # cleaning up .sra file... | ||
| echo "mkdir data # cleaning up .sra file..." >> run.bash | ||
| mv ${id_file}_1.fastq.gz data/; ln -s data/${id_file}_1.fastq.gz ${name_sample}_L${num_run}_R1.fastq.gz # linking read1... | ||
| echo "mv ${id_file}_1.fastq.gz data/; ln -s data/${id_file}_1.fastq.gz ${name_sample}_L${num_run}_R1.fastq.gz # linking read1..." >> run.bash | ||
| echo " | | Linking data/${id_file}_1.fastq.gz to ${name_sample}_L${num_run}_R1.fastq.gz" | ||
| if [[ -f ${id_file}_2.fastq.gz ]] | ||
| then | ||
| mv ${id_file}_2.fastq.gz data/; ln -s data/${id_file}_2.fastq.gz ${name_sample}_L${num_run}_R2.fastq.gz # linking read2... | ||
| echo "mv ${id_file}_2.fastq.gz data/; ln -s data/${id_file}_2.fastq.gz ${name_sample}_L${num_run}_R2.fastq.gz # linking read2..." >> run.bash | ||
| echo " | | Linking data/${id_file}_2.fastq.gz to ${name_sample}_L${num_run}_R2.fastq.gz" | ||
| fi | ||
| done | ||
| done | ||
| elif [[ $header == *gdc-user-token* ]] | ||
| then | ||
| echo | ||
| echo "###### Downloading $name_sample from TCGA!" | ||
| echo $id_sample | ||
| echo " |____ Downloading .bam file..." | ||
| cd ../;$gdc_client_path download --no-annotations -n $NSLOTS -t $header $id_sample;cd -;mkdir data # Downloading bam file and creating data directory... | ||
| echo "cd ../;$gdc_client_path download --no-annotations -n $NSLOTS-t $header $id_sample;cd -;mkdir data # Downloading bam file and creatingi data directory... " >> run.bash | ||
| echo " |____ Converting to .fastq file..." | ||
| java -jar $picard_path SamToFastq I=`ls *.bam` FASTQ=data/${id_sample}_L001_R1.fastq SECOND_END_FASTQ=data/${id_sample}_L001_R2.fastq QUIET=true VERBOSITY=ERROR INCLUDE_NON_PF_READS=true # Converting to fastq file... | ||
| echo "java -jar $picard_path SamToFastq I=\`ls *.bam\` FASTQ=data/${id_sample}_L001_R1.fastq SECOND_END_FASTQ=data/${id_sample}_L001_R2.fastq QUIET=true VERBOSITY=ERROR INCLUDE_NON_PF_READS=true # Converting to fastq file..." >> run.bash | ||
| rm -rf *.ba{m,i} # Cleaning up .bam and .bai file | ||
| echo "rm -rf *.ba{m,i} # cleaning up .bam and .bai file" >> run.bash | ||
| echo " |____ Gzipping to .gz file..." | ||
| gzip data/${id_sample}_L001_R1.fastq data/${id_sample}_L001_R2.fastq # Gzipping to .gz file... | ||
| echo "gzip data/${id_sample}_L001_R1.fastq data/${id_sample}_L001_R2.fastq # Gzipping to .gz file..." >> run.bash | ||
| ln -s data/${id_sample}_L001_R1.fastq.gz ${name_sample}_L001_R1.fastq.gz # Linking read1... | ||
| echo "ln -s data/${id_sample}_L001_R1.fastq.gz ${name_sample}_L001_R1.fastq.gz # Linking read1..." >> run.bash | ||
| if [ ! -s data/${id_sample}_L001_R2.fastq.gz ] | ||
| then | ||
| rm -rf data/${id_sample}_L001_R2.fastq.gz # Deleting empty read2 file... | ||
| echo "rm -rf data/${id_sample}_L001_R2.fastq.gz # Deleting empty read2 file..." >> run.bash | ||
| else | ||
| ln -s data/${id_sample}_L001_R2.fastq.gz ${name_sample}_L001_R2.fastq.gz # Linking read2... | ||
| echo "ln -s data/${id_sample}_L001_R2.fastq.gz ${name_sample}_L001_R2.fastq.gz # Linking read2..." >> run.bash | ||
| fi | ||
| elif [ -d $header ] | ||
| then | ||
| echo | ||
| echo "###### Linking $name_sample from Local Directory!" | ||
| echo $header | ||
| ln -s $header data # linking source directory... | ||
| echo "ln -s $header data # linking source directory..." >> run.bash | ||
| for myfastq in `ls -1 $header | grep "$id_sample"` | ||
| do | ||
| echo " |____ data/`basename $myfastq` to ${name_sample}`echo $myfastq | sed 's/'$id_sample'/\t/g' | cut -f2`" | ||
| ln -sf data/`basename $myfastq` ${name_sample}`echo $myfastq | sed 's/'$id_sample'/\t/g' | cut -f2` # linking file... | ||
| echo "ln -sf data/\`basename $myfastq\` ${name_sample}\`echo $myfastq | sed 's/'$id_sample'/\t/g' | cut -f2\` # linking file..." >> run.bash | ||
| done | ||
| else | ||
| printf "\n###### Metadata file lacking of comment header! \n\t(The first line of input metadata file should start with \"\# \" and follow by \" SRA\", \"TCGA\", or local directory path\n" | ||
| fi | ||
| fi | ||
| echo "cd $CWD # changing back to working directory..." >> run.bash | ||
| cd $CWD | ||
| done | ||
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| ######################### | ||
| echo | ||
| date | ||
| # end |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,11 @@ | ||
| #!/usr/bin/env Rscript | ||
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| list.of.packages=c("tools","DESeq2","GenomicFeatures","dplyr","BiocParallel","pheatmap","RColorBrewer","ggplot2","ReportingTools","hwriter","reshape2","preprocessCore","cowplot","diagram","GGally","tidyr","animation") | ||
| list.of.packages=c("EDASeq","ggthemes","TxDb.Hsapiens.UCSC.hg19.knownGene","TCGAbiolinks","tools","DESeq2","GenomicFeatures","dplyr","BiocParallel","pheatmap","RColorBrewer","ggplot2","ReportingTools","hwriter","reshape2","preprocessCore","cowplot","diagram","GGally","tidyr","animation") | ||
| missing.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])] | ||
| for (p in missing.packages){ | ||
| if(!file.exists(Sys.getenv("R_LIBS_USER"))){ | ||
| system(paste0("mkdir -p ",Sys.getenv("R_LIBS_USER"))) | ||
| } | ||
| source("https://bioconductor.org/biocLite.R") | ||
| biocLite(p,lib=Sys.getenv("R_LIBS_USER")) | ||
| source("http://bioconductor.org/biocLite.R") | ||
| biocLite(p,lib=Sys.getenv("R_LIBS_USER"),suppressUpdates=TRUE) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| #!/local/apps/python/2.7.3/bin/python | ||
| # EASY-INSTALL-SCRIPT: 'gdc-client==1.2.0','gdc-client' | ||
| __requires__ = 'gdc-client==1.2.0' | ||
| __import__('pkg_resources').run_script('gdc-client==1.2.0', 'gdc-client') |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| picard-2.9.0.jar |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| EryB SRX669497 SRA | ||
| f327cd15-9af4-4c6d-8318-986934ea32c9 f327cd15-9af4-4c6d-8318-986934ea32c9 meta_data/gdc-user-token.xxxxxx.txt | ||
| A549_REN_24H-rep1 A549_REN_REP1_24H_CGATGT /ifs/data/2016-02-24/fastq/ | ||
| EryA SRX669496 SRA | ||
| e3878649-03e0-4d19-a14c-344afe2f1b4a e3878649-03e0-4d19-a14c-344afe2f1b4a meta_data/gdc-user-token.xxxxxx.txt | ||
| A549_REN_48H-rep1 A549_REN_REP1_48H_CGATGT /ifs/data/2016-02-24/fastq/ |
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