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stajichlab / FGMP

Fungal Genome Mapping Pipeline
MIT License
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problem with conda installation #12

Closed asteindorff closed 4 years ago

asteindorff commented 5 years ago

I installed the program using conda, but I get this error when I try to run:

Can't locate FGMP.pm in @INC (you may need to install the FGMP module)

I tried to add the FGPM module in my @INC, no success.

ocisse commented 5 years ago

Thanks. It looks like something like the following code is missing in the bioconda recipe ln -s ${FGMP_HOME}/lib/FGMP.pm ${PREFIX}/lib/FGMP.pm

here is a temporary fix: export PERL5LIB="$PERL5LIB:/Users/cisseoh/anaconda3/share/fgmp-1.0.3-0/lib"

hyphaltip commented 5 years ago

Ill see if I can fix the recipe in bioconda thanks for the report.

Jason E Stajich, PhD Professor and Director, Microbiology Graduate Program Dept of Microbiology and Plant Pathology University of California, Riverside http://lab.stajich.org @stajichlab @hyphaltip @zygolife +1 951.827.2363 On Apr 19, 2019, 6:02 PM -0700, noreply@github.com, wrote:

Thanks. It looks like something like the following code is missing in the bioconda recipe ln -s ${FGMP_HOME}/lib/FGMP.pm ${PREFIX}/lib/FGMP.pm here is a temporary fix: export PERL5LIB="$PERL5LIB:/Users/cisseoh/anaconda3/share/fgmp-1.0.3-0/lib" — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

molecules commented 5 years ago

My quick fix was going to path/to/lib/5.26.2 and creating a link, thus:

ln -s path/to/share/fgmp-1.0.3-0/lib/FGMP.pm

hyphaltip commented 5 years ago

thanks - I have not had a chance to make the conda fix but I can talk with Brad there about making sure we do it correctly.

Jason E Stajich, PhD Professor and Director, Microbiology Graduate Program Department of Microbiology and Plant Pathology University of California, Riverside http://lab.stajich.org @stajichlab @hyphaltip @zygolife +1 951.827.2363

On Tue, Apr 30, 2019 at 1:41 PM Christopher Bottoms < notifications@github.com> wrote:

My quick fix was going to path/to/lib/5.26.2 and creating a link, thus:

ln -s path/to/share/fgmp-1.0.3-0/lib/FGMP.pm

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stajichlab/FGMP/issues/12#issuecomment-488107508, or mute the thread https://github.com/notifications/unsubscribe-auth/AAAL5O5JPTCDLBKPH4Z4VQDPTCVIBANCNFSM4HHIOFVQ .

emmannaemeka commented 4 years ago

Had similar issue tried using the temporary fix export PERL5LIB="$PERL5LIB:/opt/anaconda3/envs/fgmp/sharefgmp-1.0.3-1/lib"

Error Can't locate FGMP.pm in @INC (you may need to install the FGMP module) (@INC contains: /opt/anaconda3/envs/fgmp/bin/lib /opt/anaconda3/envs/fgmp/bin/../lib/5.26.2/darwin-thread-multi-2level /opt/anaconda3/envs/fgmp/bin/../lib/5.26.2 /opt/anaconda3/envs/fgmp/bin/../lib /Users/cisseoh/anaconda3/share/fgmp-1.0.3-0/lib /opt/anaconda3/envs/fgmp/sharefgmp-1.0.3-1/lib /opt/anaconda3/envs/fgmp/lib/site_perl/5.26.2/darwin-thread-multi-2level /opt/anaconda3/envs/fgmp/lib/site_perl/5.26.2 /opt/anaconda3/envs/fgmp/lib/5.26.2/darwin-thread-multi-2level /opt/anaconda3/envs/fgmp/lib/5.26.2 .) at /opt/anaconda3/envs/fgmp/bin/fgmp line 41.

hyphaltip commented 4 years ago

We will to get this fixed in conda.

Jason E Stajich, PhD Professor and Director, Microbiology Graduate Program Dept of Microbiology and Plant Pathology University of California, Riverside

Fellow, CIFAR Fungal Kingdom: Threats & Opportunities email: jason.stajich@ucr.edu twitter: @stajichlab@hyphaltip@zygolife website: lab.stajich.org phone: +1 951.827.2363 On Dec 10, 2019, 5:08 PM -0800, emmannaemeka notifications@github.com, wrote:

Had similar issue tried using the temporary fix export PERL5LIB="$PERL5LIB:/opt/anaconda3/envs/fgmp/sharefgmp-1.0.3-1/lib" Error Can't locate FGMP.pm in @inc (you may need to install the FGMP module) (@inc contains: /opt/anaconda3/envs/fgmp/bin/lib /opt/anaconda3/envs/fgmp/bin/../lib/5.26.2/darwin-thread-multi-2level /opt/anaconda3/envs/fgmp/bin/../lib/5.26.2 /opt/anaconda3/envs/fgmp/bin/../lib /Users/cisseoh/anaconda3/share/fgmp-1.0.3-0/lib /opt/anaconda3/envs/fgmp/sharefgmp-1.0.3-1/lib /opt/anaconda3/envs/fgmp/lib/site_perl/5.26.2/darwin-thread-multi-2level /opt/anaconda3/envs/fgmp/lib/site_perl/5.26.2 /opt/anaconda3/envs/fgmp/lib/5.26.2/darwin-thread-multi-2level /opt/anaconda3/envs/fgmp/lib/5.26.2 .) at /opt/anaconda3/envs/fgmp/bin/fgmp line 41. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

ocisse commented 4 years ago

Sure -

"Had similar issue tried using the temporary fix export PERL5LIB="$PERL5LIB:/opt/anaconda3/envs/fgmp/sharefgmp-1.0.3-1/lib"" Which system are you using? what happens if you copy the lib file in the directory where the main script is?