Public | Automated Build

Last pushed: 8 months ago
Short Description
OpenMS-based scripts to reproduce MTBLS233. This container natively supports HDFS.
Full Description

OpenMS - Swift container - MTBLS233

This container adds script folder bin/ that handles downloading and uploading with Swift obect storage and executing openMS commands

OpenMS.py is handling the down and uploading of files from Swift object storage. OpenMS.py is also running the openMS command specified as argument, and replacing the tags {infile} {outfile} with the local files checked out by the from swift storage. The files to be downloaded and uploaded with swift are specified as environment variables, -e "infile=testfile.txt" -e "outfile=result.txt" -e "swift_container_input=anders-test" -e "swift_container_output=anders-test"

You can provide parameters to the docker container as separate environment parameters as in PeakPickerHiRes example below, or all parameters in one environment parameter named "envparams" with all (sub)-parameters provided as a comma separated string, as in example FeatureFinderMetabo

This container also adds OpenMS parameters for analysis MTBLS233 in directory /params_MTBLS233

Build container

docker build -t farmbio/mtbls233-openms .

Run container

PeakPickerHiRes

docker run --rm -e "infile=testfile.txt" -e "outfile=result.txt" -e "swift_container_input=anders-test" -e "swift_container_output=anders-test" -e "OS_AUTH_URL=https://identity1.citycloud.com:5000/v3/" -e "OS_AUTH_VERSION=3" -e "OS_TENANT_NAME=your-tenant-name" -e "OS_TENANT_ID=17bcdf88f1fd40de85f53b5038722681" -e "OS_REGION_NAME=Lon1" -e "OS_DOMAIN_ID=08ba9f88ca5647b0ad4d651698eef3d0" -e "OS_USER_DOMAIN_ID=08ba9f88ca5647b0ad4d651698eef3d0" -e "OS_USERNAME=your-username" -e "OS_PASSWORD=your-password" farmbio/mtbls233-openms /bin/OpenMS.py PeakPickerHiRes -in {infile} -out {outfile} -ini /params_MTBLS233/PPparam.ini

FeatureFinderMetabo

docker run --rm -e "envparams=infile=testfile.txt,outfile=result.txt,swift_container_input=anders-test,swift_container_output=anders-test,OS_AUTH_URL=https://identity1.citycloud.com:5000/v3/,OS_AUTH_VERSION=3,OS_TENANT_NAME=your-tenant-name,OS_TENANT_ID=17bcdf88f1fd40de85f53b5038722681,OS_REGION_NAME=Lon1,OS_DOMAIN_ID=08ba9f88ca5647b0ad4d651698eef3d0,OS_USER_DOMAIN_ID=08ba9f88ca5647b0ad4d651698eef3d0,OS_USERNAME=your-username,OS_PASSWORD=your-password" farmbio/mtbls233-openms /bin/OpenMS.py FeatureFinderMetabo -in {infile} -out {outfile} -ini /params_MTBLS233/FFparam.ini

FeatureLinkerUnlabeledQT

docker run --rm -e "infile=testfile.txt" -e "outfile=result.txt" -e "swift_container_input=anders-test" -e "swift_container_output=anders-test" -e "OS_AUTH_URL=https://identity1.citycloud.com:5000/v3/" -e "OS_AUTH_VERSION=3" -e "OS_TENANT_NAME=your-tenant-name" -e "OS_TENANT_ID=17bcdf88f1fd40de85f53b5038722681" -e "OS_REGION_NAME=Lon1" -e "OS_DOMAIN_ID=08ba9f88ca5647b0ad4d651698eef3d0" -e "OS_USER_DOMAIN_ID=08ba9f88ca5647b0ad4d651698eef3d0" -e "OS_USERNAME=your-username" -e "OS_PASSWORD=your-password" farmbio/mtbls233-openms /bin/OpenMS.py FeatureLinkerUnlabeledQT -in {infile} -out {outfile} -ini /params_MTBLS233/FLparam.ini

FileFlter

docker run --rm -e "infile=testfile.txt" -e "outfile=result.txt" -e "swift_container_input=anders-test" -e "swift_container_output=anders-test" -e "OS_AUTH_URL=https://identity1.citycloud.com:5000/v3/" -e "OS_AUTH_VERSION=3" -e "OS_TENANT_NAME=your-tenant-name" -e "OS_TENANT_ID=17bcdf88f1fd40de85f53b5038722681" -e "OS_REGION_NAME=Lon1" -e "OS_DOMAIN_ID=08ba9f88ca5647b0ad4d651698eef3d0" -e "OS_USER_DOMAIN_ID=08ba9f88ca5647b0ad4d651698eef3d0" -e "OS_USERNAME=your-username" -e "OS_PASSWORD=your-password" farmbio/mtbls233-openms /bin/OpenMS.py FileFilter -in {infile} -out {outfile} -ini /params_MTBLS233/FileFparam.ini

TextExporter

docker run --rm -e "infile=testfile.txt" -e "outfile=result.txt" -e "swift_container_input=anders-test" -e "swift_container_output=anders-test" -e "OS_AUTH_URL=https://identity1.citycloud.com:5000/v3/" -e "OS_AUTH_VERSION=3" -e "OS_TENANT_NAME=your-tenant-name" -e "OS_TENANT_ID=17bcdf88f1fd40de85f53b5038722681" -e "OS_REGION_NAME=Lon1" -e "OS_DOMAIN_ID=08ba9f88ca5647b0ad4d651698eef3d0" -e "OS_USER_DOMAIN_ID=08ba9f88ca5647b0ad4d651698eef3d0" -e "OS_USERNAME=your-username" -e "OS_PASSWORD=your-password" farmbio/mtbls233-openms /bin/OpenMS.py TextExporter -in {infile} -out {outfile} -ini /params_MTBLS233/TEparam.ini

Run interactive for testing

```bash
docker run -it farmbio/mtbls233-openms /bin/bash

Docker Pull Command
Owner
farmbio
Source Repository

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