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TrinityCTAT / ctat-mutations

Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
https://github.com/TrinityCTAT/ctat-mutations
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k8 missing from Container #128

Closed readline closed 9 months ago

readline commented 9 months ago

In the version 4.0.0, the step of mutation lib integration, script ctat-mutation-lib-integration.py will call paftools.ctat.js. k8 is required to execute the js script. However, the Docker/singularity image doesn't have it installed, thus, causing the error:

/usr/bin/env: ‘k8’: No such file or directory
brianjohnhaas commented 9 months ago

sorry - just a sec and I'll add it.

On Tue, Oct 3, 2023 at 3:38 PM Kai Yu @.***> wrote:

In the version 4.0.0, the step of mutation lib integration, script ctat-mutation-lib-integration.py will call paftools.ctat.js. k8 is required to execute the js script. However, the Docker/singularity image doesn't have it installed, thus, causing the error:

/usr/bin/env: ‘k8’: No such file or directory

— Reply to this email directly, view it on GitHub https://github.com/NCIP/ctat-mutations/issues/128, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX5YYCT46TFFPO5T3MTX5RSRZAVCNFSM6AAAAAA5RPWQWKVHI2DSMVQWIX3LMV43ASLTON2WKOZRHEZDIOBRHAYTQNI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

brianjohnhaas commented 9 months ago

Should be added now. Please try again.

best,

~b

On Tue, Oct 3, 2023 at 3:40 PM Brian Haas @.***> wrote:

sorry - just a sec and I'll add it.

On Tue, Oct 3, 2023 at 3:38 PM Kai Yu @.***> wrote:

In the version 4.0.0, the step of mutation lib integration, script ctat-mutation-lib-integration.py will call paftools.ctat.js. k8 is required to execute the js script. However, the Docker/singularity image doesn't have it installed, thus, causing the error:

/usr/bin/env: ‘k8’: No such file or directory

— Reply to this email directly, view it on GitHub https://github.com/NCIP/ctat-mutations/issues/128, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX5YYCT46TFFPO5T3MTX5RSRZAVCNFSM6AAAAAA5RPWQWKVHI2DSMVQWIX3LMV43ASLTON2WKOZRHEZDIOBRHAYTQNI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

brianjohnhaas commented 9 months ago

Note, I didn't update the singularity image yet. I'll do that shortly

On Tue, Oct 3, 2023 at 3:44 PM Brian Haas @.***> wrote:

Should be added now. Please try again.

best,

~b

On Tue, Oct 3, 2023 at 3:40 PM Brian Haas @.***> wrote:

sorry - just a sec and I'll add it.

On Tue, Oct 3, 2023 at 3:38 PM Kai Yu @.***> wrote:

In the version 4.0.0, the step of mutation lib integration, script ctat-mutation-lib-integration.py will call paftools.ctat.js. k8 is required to execute the js script. However, the Docker/singularity image doesn't have it installed, thus, causing the error:

/usr/bin/env: ‘k8’: No such file or directory

— Reply to this email directly, view it on GitHub https://github.com/NCIP/ctat-mutations/issues/128, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX5YYCT46TFFPO5T3MTX5RSRZAVCNFSM6AAAAAA5RPWQWKVHI2DSMVQWIX3LMV43ASLTON2WKOZRHEZDIOBRHAYTQNI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

brianjohnhaas commented 9 months ago

singularity image is now updated as well

On Tue, Oct 3, 2023 at 3:45 PM Brian Haas @.***> wrote:

Note, I didn't update the singularity image yet. I'll do that shortly

On Tue, Oct 3, 2023 at 3:44 PM Brian Haas @.***> wrote:

Should be added now. Please try again.

best,

~b

On Tue, Oct 3, 2023 at 3:40 PM Brian Haas @.***> wrote:

sorry - just a sec and I'll add it.

On Tue, Oct 3, 2023 at 3:38 PM Kai Yu @.***> wrote:

In the version 4.0.0, the step of mutation lib integration, script ctat-mutation-lib-integration.py will call paftools.ctat.js. k8 is required to execute the js script. However, the Docker/singularity image doesn't have it installed, thus, causing the error:

/usr/bin/env: ‘k8’: No such file or directory

— Reply to this email directly, view it on GitHub https://github.com/NCIP/ctat-mutations/issues/128, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX5YYCT46TFFPO5T3MTX5RSRZAVCNFSM6AAAAAA5RPWQWKVHI2DSMVQWIX3LMV43ASLTON2WKOZRHEZDIOBRHAYTQNI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

readline commented 9 months ago

Problem solved! Thanks for the lightning quick patch