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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
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RepeatMasker not configuring within Maker bioconda recipe #30124

Open AdamStuckert opened 3 years ago

AdamStuckert commented 3 years ago

Hi all,

This seems to be an issue that is popping up now and again (e.g., https://github.com/bioconda/bioconda-recipes/issues/25559). This was supposedly fixed, but I'm seeing it again.

The issue is that when I try to configure RepeatMasker I am getting the following error:

No repeat libraries found!  At a minimum Dfam.embl, Dfam.hmm
or RepBase RepeatMasker Edition is required to run.  Please download
 and install the latest Dfam libraries.

However, I downloaded the DFAM database, and as you can see it is in the appropriate Libraries directory:

(maker) [astuck@longleaf-login2 RepeatMasker]$ lr Libraries/
total 2.4G
-rw-rw-r-- 4 astuck rc_matutelb_psx  18M May  6 17:29 RMRBMeta.embl
-rw-rw-r-- 4 astuck rc_matutelb_psx 109M May  6 17:29 taxonomy.dat
-rw-rw-r-- 4 astuck rc_matutelb_psx 5.5K May  6 17:29 RepeatPeps.readme
-rw-rw-r-- 4 astuck rc_matutelb_psx  18M May  6 17:29 RepeatPeps.lib
-rwxrwxr-x 4 astuck rc_matutelb_psx  25K May  6 17:29 Artefacts.embl
-rw-rw-r-- 4 astuck rc_matutelb_psx  214 May  6 17:30 README.meta
-rw-rw-r-- 4 astuck rc_matutelb_psx 1.9G May  6 17:30 Dfam.h5
-rwxrwxr-x 4 astuck rc_matutelb_psx  22M May  6 17:30 RepeatAnnotationData.pm
-rw-rw-r-- 4 astuck rc_matutelb_psx  23M Aug 11 17:09 RepeatMasker.lib
lrwxrwxrwx 1 astuck rc_matutelb_psx   96 Aug 17 15:24 RepeatMaskerLib.h5 -> /proj/matutelb/users/stuckert/software/anaconda3/envs/maker/share/RepeatMasker/Libraries/Dfam.h5
-rw-r--r-- 1 astuck rc_matutelb_psx 179K Aug 17 15:24 RepeatMasker.lib.nin
-rw-r--r-- 1 astuck rc_matutelb_psx 1.6M Aug 17 15:24 RepeatMasker.lib.nhr
-rw-r--r-- 1 astuck rc_matutelb_psx 6.0M Aug 17 15:24 RepeatMasker.lib.nsq
-rw-r--r-- 1 astuck rc_matutelb_psx 141K Aug 17 15:24 RepeatPeps.lib.pin
-rw-r--r-- 1 astuck rc_matutelb_psx 2.8M Aug 17 15:24 RepeatPeps.lib.phr
-rw-r--r-- 1 astuck rc_matutelb_psx  16M Aug 17 15:24 RepeatPeps.lib.psq
drwxr-sr-x 2 astuck rc_matutelb_psx  139 Aug 17 16:32 general

I have tried setting LIBDIR manually with export LIBDIR= per suggestions in other issues threads, but this also does not help. I am using RepeatMasker version 4.1.2-p1.

Anyone have any insight?

MagnusKerber commented 3 years ago

Hi! I had a similar issue, and exported LIBDIR as:

export LIBDIR=path/to/conda/env/share/RepeatMasker/Libraries

This worked for me. How did you export yours? Seems like you are using conda and built a specific environment for "Maker", I did that as well.

Cheers,

AdamStuckert commented 3 years ago

I did that as well, both the Maker specific environment and export LIBDIR. @MagnusKerber what version of RepeatMasker is in your conda environment?

MagnusKerber commented 3 years ago

Hi @AdamStuckert, my version is the 2.0.1. It came along with the Maker recipe in conda, maybe that's your issue.

MagnusKerber commented 3 years ago

@AdamStuckert was the issue solved?

AdamStuckert commented 3 years ago

Negative, this did not solve my issue. I'm attempting a clean install of maker, but it keeps failing to solve the environment. Once the install works I'll chime back in.