prep_genome_lib.pl: No such file or directory

[gremame]

Hello Brian,
I tried to run the tutorial but got an error message in the first step (using Docker):

${STAR_FUSION_HOME}/FusionFilter/prep_genome_lib.pl \
        --genome_fa minigenome.fa \
        --gtf minigenome.gtf \
        --fusion_annot_lib CTAT_HumanFusionLib.mini.dat.gz

The error message is the following
bash: /usr/local/src/STAR-Fusion/FusionFilter/prep_genome_lib.pl: No such file or directory

There seems to be no prep_genome_lib.pl file.
Cheers!
David

[brianjohnhaas]

Hi David, You can use the version of the Docker image that was available at the time the tutorial was made. I need to update it for the next release (later in August), as some parts have moved around. best, ~brian

…

On Fri, Jul 26, 2019 at 6:04 AM gremame ***@***.***> wrote: Hello Brian, I tried to run the tutorial but got an error message in the first step (using Docker): ${STAR_FUSION_HOME}/FusionFilter/prep_genome_lib.pl \ --genome_fa minigenome.fa \ --gtf minigenome.gtf \ --fusion_annot_lib CTAT_HumanFusionLib.mini.dat.gz The error message is the following bash: /usr/local/src/STAR-Fusion/FusionFilter/prep_genome_lib.pl: No such file or directory There seems to be no prep_genome_lib.pl file. Cheers! David — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=ABZRKX56SKIB3X7TUJWIOHTQBLD2ZA5CNFSM4IHCMZGKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HBVWGWQ>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZRKXZRHLQ324O2IMT6F4DQBLD2ZANCNFSM4IHCMZGA> .

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

[aleksicmil]

Dear Brian,

I am using the Dockerfile available within the latest release, and I am seeing the same error:

prep_genome_lib.pl: not found
Has this issue bin fixed in the meantime, or should I use some of the earlier docker files?

Thanks!

Milica

[brianjohnhaas]

Hi The tutorial hasn't been updated to work with the latest version. I neglected to do this... If you pull an earlier docker that was available at the time the tutorial was written, should hopefully work. Leave this open and I'll work on updating it. Thx

…

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On Wed, Dec 11, 2019, 10:21 AM aleksicmil ***@***.***> wrote: Dear Brian, I am using the Dockerfile available within the latest release, and I am seeing the same error: prep_genome_lib.pl: not found Has this issue bin fixed in the meantime, or should I use some of the earlier docker files? Thanks! Milica — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=ABZRKX2AR2FXO6H7ZGHEYVLQYEARBA5CNFSM4IHCMZGKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGTQHFA#issuecomment-564593556>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX65UMEIJOG7GXTKVF3QYEARBANCNFSM4IHCMZGA> .