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Picard in Docker
Dear GATK/Picard team,
I am new to Picard and was just about to build it, when I noticed that there is a Picard Docker image available - great idea! Is this functional yet? I couldn't find any instructions on how to use it. I gave it a try and did the following:
pulled the picard image
docker pull broadinstitute/picard
then I am trying to run it like so:
docker run -i -t broadinstitute/picard FastqToSam -h
This gives me the usage for FastqToSam so I thought I was on the right track.
However, when running a full fetched command like:
sudo docker run -i -t broadinstitute/picard FastqToSam F1=009_S1_L001_R1_001.fastq.gz F2=009_S1_L001_R2_001.fastq.gz O=test.bam SM=female
I get the following error:
[Tue Aug 25 20:09:49 UTC 2015] picard.sam.FastqToSam FASTQ=009_S1_L001_R1_001.fastq.gz FASTQ2=F1=009_S1_L001_R2_001.fastq.gz OUTPUT=test.bam SAMPLE_NAME=female USE_SEQUENTIAL_FASTQS=false READ_GROUP_NAME=A SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 25 20:09:49 UTC 2015] Executing as [email protected] on Linux 3.13.0-54-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.138() JdkDeflater
[Tue Aug 25 20:09:49 UTC 2015] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: /usr/picard/009_S1_L001_R1_001.fastq.gz
It seems as if Picard in the container can't find my input files. How would I pass my files correctly to the container?
Any help would be much appreciated!!
Thanks in advance for your time!