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Merge pull request #26 from icgc-argo/ega-download-wf@0.1.3
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ega_file_id path |
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ega_file_id path | ||
EGAF00001770106 EGAF00001770106.bam | ||
EGAF00001770106 |
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{ | ||
"file_info_tsv" : "tests/input/pyega3.tsv", | ||
"pyega3_ega_user" : "ega-test-data@ebi.ac.uk", | ||
"pyega3_ega_pass" : "egarocks", | ||
"download_mode" : "aspera", | ||
"ascp_scp_host" : "", | ||
"ascp_scp_user" : "", | ||
"aspera_scp_pass" : "" | ||
"file_info_tsv" : "input/aspera.tsv", | ||
"download_mode" : "aspera" | ||
} |
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{ | ||
"file_info_tsv" : "tests/input/pyega3.tsv", | ||
"file_info_tsv" : "input/pyega3.tsv", | ||
"pyega3_ega_user" : "ega-test-data@ebi.ac.uk", | ||
"pyega3_ega_pass" : "egarocks", | ||
"download_mode" : "pyega3", | ||
"ascp_scp_host" : "", | ||
"ascp_scp_user" : "", | ||
"aspera_scp_pass" : "" | ||
"download_mode" : "pyega3" | ||
} |
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wfpr_modules/github.com/icgc-argo/argo-data-submission/decrypt-aspera@0.1.1/.dockerignore
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.gitignore | ||
.nextflow* | ||
tests | ||
work | ||
outdir |
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wfpr_modules/github.com/icgc-argo/argo-data-submission/decrypt-aspera@0.1.1/Dockerfile
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FROM ubuntu:18.04 | ||
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LABEL org.opencontainers.image.source https://github.com/icgc-argo/argo-data-submission | ||
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LABEL org.opencontainers.image.authors Edmund Su (edmund.su@oicr.on.ca) | ||
LABEL org.opencontainers.image.title ICGC ARGO Data Decrypt files | ||
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RUN apt-get update && \ | ||
apt-get install -y python3-pip python3-dev software-properties-common curl python3-setuptools && \ | ||
apt-get install -y libz-dev pkg-config libtool m4 autotools-dev automake libncurses5-dev libbz2-dev liblzma-dev | ||
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RUN pip3 install --upgrade pip &&\ | ||
pip3 install numpy crypt4gh | ||
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RUN mkdir /tools | ||
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ENV PATH="/tools:${PATH}" | ||
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COPY *.py /tools/ | ||
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RUN groupadd -g 1000 ubuntu &&\ | ||
useradd -l -u 1000 -g ubuntu ubuntu &&\ | ||
install -d -m 0755 -o ubuntu -g ubuntu /home/ubuntu | ||
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ENV PATH="/tools:${PATH}" | ||
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COPY *.py /tools/ | ||
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ENTRYPOINT ["/usr/bin/env"] | ||
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USER ubuntu | ||
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CMD ["/bin/bash"] |
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...odules/github.com/icgc-argo/argo-data-submission/decrypt-aspera@0.1.1/README.md
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# Package decrypt-aspera | ||
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Cryp4gh wrapper to decrypted files | ||
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## Inputs | ||
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File with the file suffix ".c4gh" | ||
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## Outputs | ||
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Decrypted file (same name without ".c4gh" suffix) | ||
Decrypted file w/ md5sum (same name with ".md5" suffix) | ||
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## Usage | ||
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#### Contents of Param-file | ||
``` | ||
{ | ||
"file":"input/mystery_file.bam.c4gh", ### File to decrypt | ||
"c4gh_secret_key":"input/C4GH_SECRET_KEY.txt", ### Public secret key | ||
"c4gh_pass_phrase":"" ### Public secret key passphrase | ||
} | ||
``` | ||
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#### Test run | ||
`nextflow run checker.nf -params-file test-job-decrypt.json` | ||
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#### IRL run | ||
``` | ||
nextflow run main.nf -params-file tests/test-job-decrypt.json | ||
``` | ||
### Run the package directly | ||
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With inputs prepared, you should be able to run the package directly using the following command. | ||
Please replace the params file with a real one (with all required parameters and input files). Example | ||
params file(s) can be found in the `tests` folder. | ||
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``` | ||
nextflow run edsu7/argo-data-submission/decrypt-aspera/main.nf -r decrypt-aspera.v0.1.0 -params-file <your-params-json-file> | ||
``` | ||
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### Import the package as a dependency | ||
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To import this package into another package as a dependency, please follow these steps at the | ||
importing package side: | ||
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1. add this package's URI `github.com/edsu7/argo-data-submission/decrypt-aspera@0.1.0` in the `dependencies` list of the `pkg.json` file | ||
2. run `wfpm install` to install the dependency | ||
3. add the `include` statement in the main Nextflow script to import the dependent package from this path: `./wfpr_modules/github.com/edsu7/argo-data-submission/decrypt-aspera@0.1.0/main.nf` |
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