RobJackson28
commented
7 years ago Job commands from an example Galaxy genotyping workflow that I saved the history of: EP FFPE Genotyping (RJ, 29 Feb 2016)
fastq files = L6R8.R1.fastq & L6R8.R2.fastq fasta file = HPVs.fasta
Step 1: python /home/galaxy/galaxy/tools/data_source/upload.py /home/galaxy/galaxy /home/galaxy/galaxy/database/tmp/tmpThv5tZ /home/galaxy/galaxy/database/tmp/tmpJJXj5j 184:/home/galaxy/galaxy/database/job_working_directory/000/184/dataset_184_files:/home/galaxy/galaxy/database/files/000/dataset_184.dat
Step 2: python /home/galaxy/galaxy/tools/data_source/upload.py /home/galaxy/galaxy /home/galaxy/galaxy/database/tmp/tmpThv5tZ /home/galaxy/galaxy/database/tmp/tmpWwDXTR 185:/home/galaxy/galaxy/database/job_working_directory/000/185/dataset_185_files:/home/galaxy/galaxy/database/files/000/dataset_185.dat
Step 3: python /home/galaxy/galaxy/tools/data_source/upload.py /home/galaxy/galaxy /home/galaxy/galaxy/database/tmp/tmpThv5tZ /home/galaxy/galaxy/database/tmp/tmpgyAbVh 186:/home/galaxy/galaxy/database/job_working_directory/000/186/dataset_186_files:/home/galaxy/galaxy/database/files/000/dataset_186.dat
Step 4: python /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/e4d28c94242d/fastq_groomer/fastq_groomer.py '/home/galaxy/galaxy/database/files/000/dataset_184.dat' 'sanger' '/home/galaxy/galaxy/database/files/000/dataset_187.dat' 'sanger' 'ascii' 'summarize_input'
Step 5: python /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/e4d28c94242d/fastq_groomer/fastq_groomer.py '/home/galaxy/galaxy/database/files/000/dataset_185.dat' 'sanger' '/home/galaxy/galaxy/database/files/000/dataset_192.dat' 'sanger' 'ascii' 'summarize_input'
Step 6: bowtie2-build "/home/galaxy/galaxy/database/files/000/dataset_186.dat" genome && ln -s "/home/galaxy/galaxy/database/files/000/dataset_186.dat" genome.fa && bowtie2 -p ${GALAXY_SLOTS:-4} -x genome -1 "/home/galaxy/galaxy/database/files/000/dataset_187.dat" -2 "/home/galaxy/galaxy/database/files/000/dataset_192.dat" | samtools view -Su - | samtools sort -o - - > /home/galaxy/galaxy/database/files/000/dataset_193.dat
Step 7: samtools view -o "/home/galaxy/galaxy/database/files/000/dataset_194.dat" -h "/home/galaxy/galaxy/database/files/000/dataset_193.dat"
Step 8: python /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/sam_bitwise_flag_filter/0b2424a404d9/sam_bitwise_flag_filter/sam_bitwise_flag_filter.py --input_sam_file=/home/galaxy/galaxy/database/files/000/dataset_194.dat --flag_column=2 '--0x0004=0' > /home/galaxy/galaxy/database/files/000/dataset_195.dat
@chgibb This is the Galaxy workflow I used for HPV genotyping, based on Holmes et al., 2016 (Holmes A, Lameiras S, Jeannot E, Marie Y, Castera L, Sastre-Garau X, Nicolas A. Mechanistic signatures of HPV insertions in cervical carcinomas. NPJ Genomic Medicine. 2016 Mar 1;1:16004.) and used in Jackson et al., 2016 (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3203-3):
I'll follow-up with command line code if I can derive from Galaxy.