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allenday / wait for operation to complete.bash
Created February 6, 2017 02:03
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
@allenday
allenday / bwa output in gs bucket.bash
Created February 6, 2017 02:08
gsutil ls -l $OUTPUT_PATH
18 2017-02-06T02:04:33Z gs://.../MNPR01.fa.amb
1576040 2017-02-06T02:04:34Z gs://.../MNPR01.fa.ann
585823748 2017-02-06T02:04:47Z gs://.../MNPR01.fa.bwt
146455918 2017-02-06T02:04:40Z gs://.../MNPR01.fa.pac
292911888 2017-02-06T02:04:38Z gs://.../MNPR01.fa.sa
TOTAL: 5 objects, 1026767612 bytes (979.2 MiB)
@allenday
allenday / align sample.bash
Created February 7, 2017 02:26
gcloud alpha genomics pipelines run \
--pipeline-file ~/src/bfx/bfx-bwa/pipeline-bwa-mem.yaml \
--logging gs://allenday-dev/bwa-logs/6/ \
--inputs INDEX_PATH=gs://$BUCKET/.../MNPR01.fa*,FASTQ_PATH=gs://$BUCKET/.../SRR4448180.fastq,PREFIX=MNPR01.fa \
--outputs OUTPUT_PATH=gs://$BUCKET/.../bam-SRR4448180/ \
@allenday
allenday / samtools_recipes.md
Last active February 22, 2017 08:21 
IS_SAM="-S"
IN=this.sam
OUT=.
# get primary alignments with unmapped mate of read pair (with header)
samtools view -h -F 0x0100 -f 0x0008 $IS_SAM $IN > $OUT/prim_mate_map.sam

# get primary alignments with unmapped self of read pair
samtools view    -F 0x0100 -f 0x0004 $IS_SAM $IN > $OUT/prim_self_map.sam
@allenday
allenday / sra_download.yaml
Created April 9, 2017 19:42
SRA download to Google Cloud Storage
name: sra_download
description: use Google Pipeline API to download an SRA run, reformat it as unaligned BAM, and upload it to Google Cloud Storage. Run it like this: gcloud alpha genomics pipelines run --inputs SAMPLE=XXXXX --inputs RUN=XXXXX --outputs OUTPUT_FILE=gs://XXXXX --pipeline-file=sra_download.yaml
resources:
#increase boot disk from 10GB to 50GB to accomodate intermediate files
bootDiskSizeGb: 50
#specify multiple zones so this pipeline will run in parallel
zones:
- us-west1-a
- us-west1-b
- us-east1-b
@allenday
allenday / assign_reserved_ip.startup_script.sh
Created April 11, 2017 21:54
#reserved static IPs on Google Cloud are named.
#specify the key EXTERNAL_IP_NAME with the correct IP name in the instance (or instance template) metadata
EXTERNAL_IP_NAME=`wget --header 'Metadata-Flavor: Google' -O - -q 'http://metadata.google.internal/computeMetadata/v1/instance/attributes/EXTERNAL_IP_NAME'`
#other metadata we can retrieve about the reserved IP and instance
EXTERNAL_IP_ADDRESS=`gcloud compute addresses list | grep $EXTERNAL_IP_NAME | awk '{print $3}'`
INSTANCE_NAME=`wget --header 'Metadata-Flavor: Google' -O - -q 'http://metadata.google.internal/computeMetadata/v1/instance/name'`
INSTANCE_ZONE=`wget --header 'Metadata-Flavor: Google' -O - -q 'http://metadata.google.internal/computeMetadata/v1/instance/zone' | cut -d/ -f4`
#delete the current IP (old access config)
yes | gcloud compute instances delete-access-config $INSTANCE_NAME --access-config-name "`yes | gcloud compute instances describe $INSTANCE_NAME --format='flattened' | grep networkInterfaces | grep accessConfigs | grep name | tai
@allenday
allenday / align_bam.yaml
Last active April 18, 2017 20:48
name: align_bam
description: use Google Pipeline API to retrieve BAMs for a given sample, align them to a reference, merge them (one BAM per RG), and upload to cloud storage
resources:
minimumCpuCores: 16
bootDiskSizeGb: 100
zones:
- us-west1-a
- us-west1-b
- us-east1-b
- us-east1-c
@allenday
allenday / samtools_index.yaml
Created May 4, 2017 17:41
name: samtools_index
description: Run samtools index to generate a BAM index file
inputParameters:
- name: INPUT_FILE
localCopy:
disk: data
path: input.bam
outputParameters:
- name: OUTPUT_FILE
localCopy:
@allenday
allenday / freebayes_vcf.yaml
Created May 5, 2017 00:03
name: freebayes_vcf
description: create .vcf, .vcf.gz, and .vcf.gz.tbi files from .bam and .bam.bai files
resources:
minimumCpuCores: 1
disks:
- name: data
type: PERSISTENT_HDD
sizeGb: 50
mountPoint: /mnt/data
zones:
@allenday
allenday / gatk_vcf.yaml
Last active May 16, 2017 03:36
name: gatk_vcf
description: create .vcf, .vcf.gz, and .vcf.gz.tbi files from .bam and .bam.bai files
resources:
minimumCpuCores: 1
disks:
- name: data
type: PERSISTENT_HDD
sizeGb: 50
mountPoint: /mnt/data
zones: