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how actually does one run your atac pipeline? super frustrated

See original GitHub issue

Hi, Glad to see that there is this ENCODE ATAC-seq pipeline. We are using some HPC to perform the computing, and as most others, we are not the admin, so a lot of times very difficult to install those packages. Anyway, I ve git clone your ‘atac-seq-pipeline’ files to folder with the same name on our HPC. We have also git cloned the Caper. I modified your minimum json input specification file to this [input.json]:

    "atac.pipeline_type" : "atac",
    "atac.genome_tsv" : "",
    "atac.fastqs_rep1_R1" : [
    "atac.fastqs_rep1_R2" : [
    "atac.paired_end" : true,
    "atac.multimapping" : 4,
    "atac.auto_detect_adapter" : true,
    "atac.trim_adapter.cpu" : 2,
    "atac.bowtie2_cpu" : 8,
    "atac.bowtie2_mem_mb" : 16000,
    "atac.filter_cpu" : 2,
    "atac.filter_mem_mb" : 12000,
    "atac.macs2_mem_mb" : 16000,
    "atac.smooth_win" : 73,
    "atac.enable_idr" : true,
    "atac.idr_thresh" : 0.05,
    "atac.enable_xcor" : true,
    "atac.title" : "Project1",
    "atac.description" : "Project1"

And then I submitted a job running this line: caper run atac.wdl -i $outdir/input.json --deepcopy --use-singularity and I got this error immediately:

usage: caper run [-h] [--dry-run] [-i INPUTS] [-o OPTIONS] [-l LABELS]
                 [-p IMPORTS] [-s STR_LABEL] [--hold]
                 [--singularity-cachedir SINGULARITY_CACHEDIR] [--no-deepcopy]
                 [--deepcopy-ext DEEPCOPY_EXT]
                 [--docker [DOCKER [DOCKER ...]]]
                 [--singularity [SINGULARITY [SINGULARITY ...]]]
                 [--no-build-singularity] [--slurm-partition SLURM_PARTITION]
                 [--slurm-account SLURM_ACCOUNT]
                 [--slurm-extra-param SLURM_EXTRA_PARAM] [--sge-pe SGE_PE]
                 [--sge-queue SGE_QUEUE] [--sge-extra-param SGE_EXTRA_PARAM]
                 [--pbs-queue PBS_QUEUE] [--pbs-extra-param PBS_EXTRA_PARAM]
                 [-m METADATA_OUTPUT] [--java-heap-run JAVA_HEAP_RUN]
                 [--db-timeout DB_TIMEOUT] [--file-db FILE_DB] [--no-file-db]
                 [--mysql-db-ip MYSQL_DB_IP] [--mysql-db-port MYSQL_DB_PORT]
                 [--mysql-db-user MYSQL_DB_USER]
                 [--mysql-db-password MYSQL_DB_PASSWORD] [--cromwell CROMWELL]
                 [--max-concurrent-tasks MAX_CONCURRENT_TASKS]
                 [--max-concurrent-workflows MAX_CONCURRENT_WORKFLOWS]
                 [--max-retries MAX_RETRIES] [--disable-call-caching]
                 [--backend-file BACKEND_FILE] [--out-dir OUT_DIR]
                 [--tmp-dir TMP_DIR] [--gcp-prj GCP_PRJ]
                 [--gcp-zones GCP_ZONES] [--out-gcs-bucket OUT_GCS_BUCKET]
                 [--tmp-gcs-bucket TMP_GCS_BUCKET]
                 [--aws-batch-arn AWS_BATCH_ARN] [--aws-region AWS_REGION]
                 [--out-s3-bucket OUT_S3_BUCKET]
                 [--tmp-s3-bucket TMP_S3_BUCKET] [--use-gsutil-over-aws-s3]
                 [-b BACKEND] [--http-user HTTP_USER]
                 [--http-password HTTP_PASSWORD] [--use-netrc]
caper run: error: argument --deepcopy-ext: expected one argument

What seems to be the problem? Seems the caper run options are different from your documentations on the landing page of this project?

We have “python3/3.6.4” and “singularity/2.5.2” loaded in out HPC.

Issue Analytics

  • State:closed
  • Created 4 years ago
  • Comments:9 (5 by maintainers)

github_iconTop GitHub Comments

akundajecommented, Sep 18, 2019

That’s not how the installation works. All dependencies are automatically installed. Jin will reply with the correct way to install the pipeline.

leepc12commented, Sep 17, 2019

We will make a release with fixed documentation soon this week. Please remove --deepcopy from the command line and use --singularity instead of --use-singularity.

Read more comments on GitHub >

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