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Last pushed: a year ago
Short Description
Seq2HLA for .bam input.
Full Description

Installed:
Ubuntu:16.04
Python 2.7.12 (pip, curl, numpy, bippython installed)
R 3.2.1
Java openjdk 1.8.0_91
bowtie 1.1.2
bam2fastq: /download/bam2fastq
repair.sh: /download/bbmap/repair.sh
seq2HLA: /download/seq2HLA.py

Usage:

step 1 bam2fastq:
/download/bam2fastq -o /workspace/${sampleID}#.fq -q /workspace/${inputBAM}.bam
gzip /workspace/${sampleID}_1.fq
gzip /workspace/${sampleID}_2.fq

step 2 repair .fq.gz files:
/download/bbmap/repair.sh in1=/workspace/${sampleID}_1.fq.gz in2=/workspace/${sampleID}_2.fq.gz out1=/workspace/${sampleID}_1.repair.fq.gz out2=/workspace/${sampleID}_2.repair.fq.gz
rm /workspace/${sampleID}_1.fq.gz /workspace/${sampleID}_2.fq.gz

step 3 run seq2HLA.py:
python /download/seq2HLA.py -1 /workspace/${sampleID}_1.repair.fq.gz -2 /workspace/${sampleID}_2.repair.fq.gz -r "/workspace/${smapleID}"

step 4 remove files:
rm /workspace/.fq /workspace/.sam /workspace/*.aligned

Docker Pull Command
Owner
jemimalwh

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