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fixed docker test file
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Sahraeian committed Nov 23, 2019
1 parent 320813b commit 0f7eb9e
Showing 1 changed file with 39 additions and 39 deletions.
78 changes: 39 additions & 39 deletions test/docker_test.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ echo "Restrict GTF to chromosome 21"
less Homo_sapiens.GRCh38.90.gtf |awk '{if ($1==21) print}' > Homo_sapiens.GRCh38.90.chromosome.21.gtf

echo "Prepare reference transcriptome FASTA file"
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 gffread \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 gffread \
/work_dir/example/Homo_sapiens.GRCh38.90.chromosome.21.gtf \
-g /work_dir/example/Homo_sapiens.GRCh38.dna.chromosome.21.fa \
-w /work_dir/example/Homo_sapiens.GRCh38.cdna.21.fa
Expand All @@ -44,12 +44,12 @@ echo "Test short-read alignment (HISAT2)"
echo "--------------------------------------------------------"
echo "--------------------------------------------------------"
echo "Index genome (chromosome 21) with HISAT2"
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 hisat2-build \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 hisat2-build \
/work_dir/example/Homo_sapiens.GRCh38.dna.chromosome.21.fa \
/work_dir/example/Homo_sapiens.GRCh38.dna.chromosome.21.HISAT2
for sample in A1 A2 B1 B2
do
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py align \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py align \
--align_idx /work_dir/example/Homo_sapiens.GRCh38.dna.chromosome.21.HISAT2 \
--outdir /work_dir/example/out \
--workdir /work_dir/example/work \
Expand All @@ -65,7 +65,7 @@ echo "--------------------------------------------------------"
echo "--------------------------------------------------------"
for sample in A1 A2 B1 B2
do
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py reconstruct \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py reconstruct \
--alignment_bam /work_dir/example/work/hisat2/${sample}/alignments.sorted.bam \
--outdir /work_dir/example/out \
--workdir /work_dir/example/work \
Expand All @@ -79,13 +79,13 @@ echo "Test quantification (Salmon-SMEM)"
echo "--------------------------------------------------------"
echo "--------------------------------------------------------"
echo "Index transcriptome with Salmon-SMEM"
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 salmon index \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 salmon index \
-t /work_dir/example/Homo_sapiens.GRCh38.cdna.21.fa \
-i /work_dir/example/Homo_sapiens.GRCh38.cdna.21.Salmon.fmd \
--type fmd
for sample in A1 A2 B1 B2
do
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py quantify \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py quantify \
--quantifier_idx /work_dir/example/Homo_sapiens.GRCh38.cdna.21.Salmon.fmd \
--1 /work_dir/${sample}_1.fq.gz \
--2 /work_dir/${sample}_2.fq.gz \
Expand All @@ -104,7 +104,7 @@ echo "Test differential expression analysis based on alignment"
echo "results(DESeq2)"
echo "--------------------------------------------------------"
echo "--------------------------------------------------------"
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py diff \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py diff \
--alignments /work_dir/example/work/hisat2/A1/alignments.sorted.bam,/work_dir/example/work/hisat2/A2/alignments.sorted.bam /work_dir/example/work/hisat2/B1/alignments.sorted.bam,/work_dir/example/work/hisat2/B2/alignments.sorted.bam \
--sample A1,A2 B1,B2 \
--ref_gtf /work_dir/example/Homo_sapiens.GRCh38.90.chromosome.21.gtf \
Expand All @@ -117,7 +117,7 @@ echo "Test differential expression analysis based on alignment-free"
echo "quantifications (DESeq2)"
echo "--------------------------------------------------------"
echo "--------------------------------------------------------"
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py diff \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py diff \
--quant_files /work_dir/example/work/salmon_smem/A1/quant.sf,/work_dir/example/work/salmon_smem/A2/quant.sf /work_dir/example/work/salmon_smem/B1/quant.sf,/work_dir/example/work/salmon_smem/B2/quant.sf \
--sample A1,A2 B1,B2 \
--ref_gtf /work_dir/example/Homo_sapiens.GRCh38.90.chromosome.21.gtf \
Expand All @@ -129,7 +129,7 @@ echo "--------------------------------------------------------"
echo "Test de novo assembly (Oases)"
echo "--------------------------------------------------------"
echo "--------------------------------------------------------"
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py denovo \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py denovo \
--1 /work_dir/A1_1.fq.gz \
--2 /work_dir/A1_2.fq.gz \
--outdir /work_dir/example/out \
Expand Down Expand Up @@ -158,7 +158,7 @@ wget http://sourceforge.net/projects/fusioncatcher/files/test/reads_1.fq.gz
wget http://sourceforge.net/projects/fusioncatcher/files/test/reads_2.fq.gz
cd ..

docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py fusion \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py fusion \
--data_dir /work_dir/example/fusioncatcher_data/human_v98/ \
--input /work_dir/example/fusioncatcher_data/reads_1.fq.gz,/work_dir/example/fusioncatcher_data/reads_2.fq.gz \
--outdir /work_dir/example/out \
Expand All @@ -172,17 +172,17 @@ echo "Test long-read error correction (LoRDEC)"
echo "--------------------------------------------------------"
echo "--------------------------------------------------------"

docker run -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py long_correct \
docker run -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py long_correct \
--kmer 23 \
--solid 3 \
--short /work_dir/example/C_short.fa \
--long /work_dir/example/C_long.fa \
--outdir /work_dir/example/out \
--workdir /work_dir/example/work \
--sample C
docker run -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 chmod -R 777 /work_dir/example/work/lordec
docker run -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 chmod -R 777 /work_dir/example/out/lordec
docker run -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 chmod -R 777 /work_dir/example/C_short.fa_k23_s3.h5
docker run -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 chmod -R 777 /work_dir/example/work/lordec
docker run -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 chmod -R 777 /work_dir/example/out/lordec
docker run -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 chmod -R 777 /work_dir/example/C_short.fa_k23_s3.h5

echo "--------------------------------------------------------"
echo "--------------------------------------------------------"
Expand All @@ -192,13 +192,13 @@ echo "--------------------------------------------------------"
echo "Index genome with STAR"
mkdir STAR_genome_index_21/
chmod -R 777 STAR_genome_index_21/
docker run -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 STAR \
docker run -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 STAR \
--runMode genomeGenerate \
--genomeDir /work_dir/example/STAR_genome_index_21/ \
--genomeFastaFiles /work_dir/example/Homo_sapiens.GRCh38.dna.chromosome.21.fa \
--runThreadN 4
docker run -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 chmod -R 777 /work_dir/example/STAR_genome_index_21
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py long_align \
docker run -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 chmod -R 777 /work_dir/example/STAR_genome_index_21
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py long_align \
--long /work_dir/example/work/lordec/C/long_corrected.fa \
--threads 4 \
--outdir /work_dir/example/out \
Expand All @@ -217,15 +217,15 @@ wget http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/refFlat.txt.gz
gunzip refFlat.txt.gz
echo "Restrict refFlat.txt annotation file to chromosome 21"
less refFlat.txt |grep chr21 |sed 's/chr21/21/g' > refFlat.21.txt
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py align \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py align \
--align_idx /work_dir/example/Homo_sapiens.GRCh38.dna.chromosome.21.HISAT2 \
--outdir /work_dir/example/out \
--workdir /work_dir/example/work \
--ref_gtf /work_dir/example/Homo_sapiens.GRCh38.90.chromosome.21.gtf \
--1 /work_dir/C_short_1.fq.gz \
--2 /work_dir/C_short_2.fq.gz \
--sample C
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py long_reconstruct \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py long_reconstruct \
--alignment /work_dir/example/work/hisat2/C/alignments.sorted.bam \
--short_junction /work_dir/example/work/hisat2/C/splicesites.bed \
--long_alignment /work_dir/example/work/starlong/C/Aligned.out.psl \
Expand Down Expand Up @@ -256,18 +256,18 @@ docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnaco
# echo "Restrict GTF to chromosome 17 and 20"
# less Homo_sapiens.GRCh37.75.gtf |awk '{if ($1==20 || $1==17) print}'|sed 's/^/chr/' > Homo_sapiens.GRCh37.75.chromosome.17_20.gtf
# echo "Index genome (chromosome 17 and 20) with HISAT2"
# docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 hisat2-build \
# docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 hisat2-build \
# /work_dir/example/MCF7_chr17q23-25chr20q13_Example/Data/genome.chr17chr20.fasta \
# /work_dir/example/MCF7_chr17q23-25chr20q13_Example/Data/genome.chr17chr20.HISAT2
# docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py align \
# docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py align \
# --align_idx /work_dir/example/MCF7_chr17q23-25chr20q13_Example/Data/genome.chr17chr20.HISAT2 \
# --outdir /work_dir/example/out \
# --workdir /work_dir/example/work \
# --ref_gtf /work_dir/example/Homo_sapiens.GRCh37.75.chromosome.17_20.gtf \
# --U /work_dir/example/MCF7_chr17q23-25chr20q13_Example/Data/short_reads.chr17q23-25chr20q13.tenth.fasta \
# --sample F \
# --hisat2_opts \"-f\"
# docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py long_fusion \
# docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py long_fusion \
# --alignment /work_dir/example/work/hisat2/F/alignments.sorted.bam \
# --short_junction /work_dir/example/work/hisat2/F/splicesites.bed \
# --long_alignment /work_dir/example/MCF7_chr17q23-25chr20q13_Example/Data/MCF7_ready_for_fusion_20140928.chr17q23-25chr20q13.sorted.psl \
Expand Down Expand Up @@ -301,22 +301,22 @@ wget ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/All_20180418.vcf.gz
gunzip All_20180418.vcf.gz
awk '{if($0 !~ /^#/) print "chr"$0; else print $0}' All_20180418.vcf |sed "s/chrMT/chrM/g" > All_20180418_chr.vcf
mv All_20180418_chr.vcf All_20180418.vcf
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 bgzip /work_dir/example/All_20180418.vcf
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 tabix /work_dir/example/All_20180418.vcf.gz
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 bgzip /work_dir/example/All_20180418.vcf
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 tabix /work_dir/example/All_20180418.vcf.gz
echo "Index reference genome FASTA file"
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 samtools faidx /work_dir/example/GRCh38_full_analysis_set_plus_decoy_hla.fa
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 java -jar /usr/local/bin/picard.jar CreateSequenceDictionary \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 samtools faidx /work_dir/example/GRCh38_full_analysis_set_plus_decoy_hla.fa
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 java -jar /usr/local/bin/picard.jar CreateSequenceDictionary \
R= /work_dir/example/GRCh38_full_analysis_set_plus_decoy_hla.fa \
O= /work_dir/example/GRCh38_full_analysis_set_plus_decoy_hla.dict
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 hisat2-build \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 hisat2-build \
/work_dir/example/GRCh38_full_analysis_set_plus_decoy_hla.fa \
/work_dir/example/GRCh38_full_analysis_set_plus_decoy_hla.HISAT2
echo "Download NA12878 FASTQ files"

wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR896/SRR896663/SRR896663_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR896/SRR896663/SRR896663_2.fastq.gz

docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py align \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py align \
--align_idx /work_dir/example/GRCh38_full_analysis_set_plus_decoy_hla.HISAT2 \
--outdir /work_dir/example/out \
--workdir /work_dir/example/work \
Expand All @@ -325,7 +325,7 @@ docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnaco
--2 /work_dir/example/SRR896663_2.fastq.gz \
--sample E \
--threads 10
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py variant \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py variant \
--alignment /work_dir/example/work/hisat2/E/alignments.sorted.bam \
--outdir /work_dir/example/out \
--workdir /work_dir/example/work \
Expand All @@ -343,7 +343,7 @@ echo "--------------------------------------------------------"
echo "Test RNA editing detection (GIREMI)"
echo "--------------------------------------------------------"
echo "--------------------------------------------------------"
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py editing \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py editing \
--alignment /work_dir/example/work/gatk/E/bsqr.bam \
--variant /work_dir/example/work/gatk/E/variants_filtered.vcf \
--strand_pos /work_dir/example/GRCh38_strand_pos.bed \
Expand All @@ -367,15 +367,15 @@ echo "denovo assembly, variant calling, and fusion detection."
echo "--------------------------------------------------------"
echo "--------------------------------------------------------"
cat <(zcat All_20180418.vcf.gz |head -10000|grep "#") <(zcat All_20180418.vcf.gz |awk '{if ($1=="chr21") print}') |sed "s/chr//g" > variants_21.vcf
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 bgzip /work_dir/example/variants_21.vcf
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 tabix /work_dir/example/variants_21.vcf.gz
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 bgzip /work_dir/example/variants_21.vcf
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 tabix /work_dir/example/variants_21.vcf.gz
cat GRCh38_genes_pos.bed |sed "s/chrM/MT/g"|sed "s/chr//g" > GRCh38_genes_pos_.bed
cat GRCh38_strand_pos.bed |sed "s/chrM/MT/g"|sed "s/chr//g" > GRCh38_strand_pos_.bed
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 samtools faidx /work_dir/example/Homo_sapiens.GRCh38.dna.chromosome.21.fa
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 java -jar /usr/local/bin/picard.jar CreateSequenceDictionary \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 samtools faidx /work_dir/example/Homo_sapiens.GRCh38.dna.chromosome.21.fa
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 java -jar /usr/local/bin/picard.jar CreateSequenceDictionary \
R= /work_dir/example/Homo_sapiens.GRCh38.dna.chromosome.21.fa \
O= /work_dir/example/Homo_sapiens.GRCh38.dna.chromosome.21.dict
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py all \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py all \
--outdir /work_dir/example/out \
--workdir /work_dir/example/work \
--threads 10 \
Expand Down Expand Up @@ -407,17 +407,17 @@ echo "variant calling and long-read error correction,"
echo "alignment, and reconstruction"
echo "--------------------------------------------------------"
echo "--------------------------------------------------------"
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 gmap_build \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 gmap_build \
-d /work_dir/example/gmap_chromosome.21 \
/work_dir/example/Homo_sapiens.GRCh38.dna.chromosome.21.fa
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 bowtie2-build \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 bowtie2-build \
/work_dir/example/Homo_sapiens.GRCh38.dna.chromosome.21.fa \
/work_dir/example/Homo_sapiens.GRCh38.dna.chromosome.21
docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 bowtie2-build \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 bowtie2-build \
/work_dir/example/Homo_sapiens.GRCh38.cdna.21.fa \
/work_dir/example/Homo_sapiens.GRCh38.cdna.21

docker run -u $UID -v=${PWD}/../:/work_dir/ rssrbred/rnacocktail:0.3.1 run_rnacocktail.py all \
docker run -u $UID -v=${PWD}/../:/work_dir/ rssbred/rnacocktail:0.3.1 run_rnacocktail.py all \
--outdir /work_dir/example/out \
--workdir /work_dir/example/work \
--threads 10 \
Expand Down

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