Question: cwl and resolution of enviroment variables
gravatar for thomas.e
3.4 years ago by
thomas.e110 wrote:


I want to make CommandLineTool to wrap the platypus variant caller. Platypus expects to invoked as:

python <arg>

In other words, by default it doesn't have a handy wrapper script. Obviously, I could write one but I thought I ought to be handle a scenario like this in CWL as follows.

In my envar-global.yml I have:

class: EnvVarRequirement
  - envName: "PLATYPUS"
    envValue: "/path/to/Platypus_0.8.1"

In my platypus.cwl, I have

baseCommand: [python, $PLATYPUS/]

However, when the command is invoked it looks the variable $PLATYPUS is not being resolved but inserted literally into the command line.

[step platyus] start
[job platyus] /stornext/HPCScratch/home/thomas.e/tmp/tmpCOMw0f$ /bin/sh \
    -c \
    'python' '$PLATYPUS/' '--bamFiles=/stornext/HPCScratch/home/thomas.e/tmp/tmpJtjVOc/stg695d99c7-792c-4f68-87da-62d472cec7c9/S1_R1.fastq.trimmed.human.sam' '--output=S1_R1.fastq.trimmed.human.vcf' '--refFile=/home/thomas.e/home/dev/Homo_sapiens.GRCh38.dna.toplevel.fa'
python: can't open file '$PLATYPUS/': [Errno 2] No such file or directory

Is the expected behaviour? Is there a correct way to handle this sort of scenario?

cwl • 1.1k views
ADD COMMENTlink modified 3.3 years ago by wolfganggerlach198150 • written 3.4 years ago by thomas.e110
gravatar for wolfganggerlach1981
3.3 years ago by
USA/Chicago/Argonne National Laboratory
wolfganggerlach198150 wrote:

This should be expected behavior. Values in baseCommand are not executed in a shell and thus environment variables not evaluated. I personally would recommend to make an executable and invoke it like this:

baseCommand: []

or if cwl-runner cannot find it:

baseCommand: [(absolute path)/]

Note: Some programming languages distinguish between ["command", "arg1"] and "command arg1". Only in the second version the command will be executed in shell and environment variables are evaluated.

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by wolfganggerlach198150
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1235 users visited in the last hour