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for B in `ls -1 *fastq* | perl -ne 'm#^(.+?)_#;print "$1\n"' | sort | uniq`; do | |
echo $B; | |
java -jar ~/bin/picard.jar FastqToSam F1=$(ls -1 ${B}_*R1*.fastq.gz) F2=$(ls -1 ${B}_*R2*fastq.gz) O=$B.bam SAMPLE_NAME=$B; | |
#in case of a failure, we'll get a file of zero bytes | |
touch $B.bam | |
done; |
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ls -l | grep -w 0 | |
-rw-r--r-- 1 root root 0 Feb 4 08:25 Black84.bam | |
-rw-r--r-- 1 root root 0 Feb 4 08:25 C4SCC.bam | |
-rw-r--r-- 1 root root 0 Feb 4 08:25 DutchHaze.bam | |
-rw-r--r-- 1 root root 0 Feb 4 08:30 GrandDaddyPurpleSCC.bam | |
-rw-r--r-- 1 root root 0 Feb 4 09:01 NorthernLightAutoFeminizedSeed.bam | |
-rw-r--r-- 1 root root 0 Feb 4 09:04 OGKushXBubbaKushSCC.bam | |
-rw-r--r-- 1 root root 0 Feb 4 09:10 OGXPurpleBubbleGumXC4SCC.bam | |
-rw-r--r-- 1 root root 0 Feb 4 09:50 SuperCritical.bam | |
-rw-r--r-- 1 root root 0 Feb 4 09:52 SuperSilverHaze.bam |
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for B in $(find * -size 0); do | |
C=${B/.bam/}; | |
echo $C; | |
java -jar ~/bin/picard.jar FastqToSam F1=$(ls -1 ${C}_*R1*.fastq.gz) O=$C.bam SAMPLE_NAME=$C; | |
done |
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gsutil -m cp *.bam gs://$BUCKET/kannapedia/ |
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#get the build specification file | |
git clone git@github.com:allenday/bfx.git | |
cd bfx/bfx-bwa | |
#do whatever you need to do | |
vim Dockerfile | |
#build it with tag bfx-bwa. you probably want to rename. | |
docker build -t bfx-bwa . |
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# Set according to your working enviroment | |
BUCKET=gs://your-bucket-name | |
WORKSPACE=$BUCKET/some/subdirectory | |
BASE_FASTA=some.fa | |
INPUT_FASTA=$BUCKET/$BASE_FASTA | |
# probably you want this to be the same as input.fasta. | |
# this is the default behavior for BWA. | |
OUTPUT_INDEX_PREFIX=$BASE_FASTA | |
OUTPUT_PATH=$WORKSPACE/out |
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OP_ID=operations/ENr3tYihKxjl8vvhnZvjmrsBIM29ta6GEioPcHJvZHVjdGlvblF1ZXVl | |
CMD="gcloud --format='value(done)' alpha genomics operations describe $OP_ID" | |
while [[ $(eval ${CMD}) != "True" ]]; do | |
echo -n "$OP_ID not done, sleeping 30s. "; | |
date; | |
sleep 30; | |
done |
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Running [operations/ENr3tYihKxjl8vvhnZvjmrsBIM29ta6GEioPcHJvZHVjdGlvblF1ZXVl] |
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operations/ENr3tYihKxjl8vvhnZvjmrsBIM29ta6GEioPcHJvZHVjdGlvblF1ZXVl not done, sleeping 30s. Sun Feb 5 17:59:53 PST 2017 | |
operations/ENr3tYihKxjl8vvhnZvjmrsBIM29ta6GEioPcHJvZHVjdGlvblF1ZXVl not done, sleeping 30s. Sun Feb 5 18:00:25 PST 2017 | |
operations/ENr3tYihKxjl8vvhnZvjmrsBIM29ta6GEioPcHJvZHVjdGlvblF1ZXVl not done, sleeping 30s. Sun Feb 5 18:00:58 PST 2017 | |
operations/ENr3tYihKxjl8vvhnZvjmrsBIM29ta6GEioPcHJvZHVjdGlvblF1ZXVl not done, sleeping 30s. Sun Feb 5 18:01:30 PST 2017 | |
operations/ENr3tYihKxjl8vvhnZvjmrsBIM29ta6GEioPcHJvZHVjdGlvblF1ZXVl not done, sleeping 30s. Sun Feb 5 18:02:01 PST 2017 | |
operations/ENr3tYihKxjl8vvhnZvjmrsBIM29ta6GEioPcHJvZHVjdGlvblF1ZXVl not done, sleeping 30s. Sun Feb 5 18:02:32 PST 2017 |
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gsutil ls -l $OUTPUT_PATH | |
18 2017-02-06T02:04:33Z gs://.../MNPR01.fa.amb | |
1576040 2017-02-06T02:04:34Z gs://.../MNPR01.fa.ann | |
585823748 2017-02-06T02:04:47Z gs://.../MNPR01.fa.bwt | |
146455918 2017-02-06T02:04:40Z gs://.../MNPR01.fa.pac | |
292911888 2017-02-06T02:04:38Z gs://.../MNPR01.fa.sa | |
TOTAL: 5 objects, 1026767612 bytes (979.2 MiB) |