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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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Fix for conda install DB_File: perl-db-file #499

Closed nextgenusfs closed 3 years ago

nextgenusfs commented 4 years ago

Conda installation might have a broken package for perl-db-file, issue on bioconda is here: https://github.com/bioconda/bioconda-recipes/issues/24688. The problem is that perl-db-file was built against an older version of libdb=6.1 while conda is installing a newer version which then causes perl-db-file to break.

This will show up if PASA/TransDecoder are failing from conda related installs. The current fix is to downgrade your libdb, ie 

conda install -n yourenv "libdb=6.1.26"
NJeanray commented 3 years ago

Hi Nextgenusfs,

I'm encountering this issue right now on conda environment and obviously I can't solve it only with libdb 6.1.26 installation.

Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: /home/ldap/NJEANRAY/anaconda3/envs/snakemake/src/STAR-Fusion/util/../PerlLib /home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/5.32/site_perl /home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/site_perl /home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/5.32/vendor_perl /home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/vendor_perl /home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/5.32/core_perl /home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/core_perl .) at /home/ldap/NJEANRAY/anaconda3/envs/snakemake/src/STAR-Fusion/util/../PerlLib/TiedHash.pm line 6.
BEGIN failed--compilation aborted at /home/ldap/NJEANRAY/anaconda3/envs/snakemake/src/STAR-Fusion/util/../PerlLib/TiedHash.pm line 6.
Compilation failed in require at /home/ldap/NJEANRAY/anaconda3/envs/snakemake/src/STAR-Fusion/util/validate_ctat_genome_lib.pl line 8.
BEGIN failed--compilation aborted at /home/ldap/NJEANRAY/anaconda3/envs/snakemake/src/STAR-Fusion/util/validate_ctat_genome_lib.pl line 8.
Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: /home/ldap/NJEANRAY/anaconda3/envs/snakemake/src/STAR-Fusion/util/../PerlLib /home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/5.32/site_perl /home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/site_perl /home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/5.32/vendor_perl /home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/vendor_perl /home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/5.32/core_perl /home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/core_perl .) at /home/ldap/NJEANRAY/anaconda3/envs/snakemake/src/STAR-Fusion/util/../PerlLib/TiedHash.pm line 6.
BEGIN failed--compilation aborted at /home/ldap/NJEANRAY/anaconda3/envs/snakemake/src/STAR-Fusion/util/../PerlLib/TiedHash.pm line 6.
Compilation failed in require at /home/ldap/NJEANRAY/anaconda3/envs/snakemake/src/STAR-Fusion/util/validate_ctat_genome_lib.pl line 8.
BEGIN failed--compilation aborted at /home/ldap/NJEANRAY/anaconda3/envs/snakemake/src/STAR-Fusion/util/validate_ctat_genome_lib.pl line 8.

Do I need to re-install something ? Or to recompile a file ?

Thanks in advance !

Best regards, Nathalie

hyphaltip commented 2 years ago

Hi - I fixed this by making sure bioconda was the preferred channel - - you want to install perl-db-file 1.855 from bioconda to get this to work

────────────────────────────────────────────────────────────────────────────
  Upgrade:
────────────────────────────────────────────────────────────────────────────

  - libdb          6.1.26  0                 bioconda
  + libdb          6.2.32  h6a678d5_1        pkgs/main/linux-64       19MB
  - perl-db-file    1.835  5                 bioconda
  + perl-db-file    1.855  pl5321h779adbc_1  bioconda/linux-64      Cached
mamba install -c bioconda perl-db-file