How To Set Db Path For Music

I'm trying to run MuSiC play but get the following error:

ERROR: Error running genome music pfam: Cannot find the pfam db path. at /gnet/resfiles3/resapps/apps/music/0.4.1-1/sles11sp2/lib/perl5/Genome/Model/Tools/Music/Pfam.pm line 89, <gen9> line 3.

I've downloaded the "genome-databases-1" folder. Where should I put the directory and how should I set my environment variable in bashrc so that MuSiC can find pfam database?

music

• 2,516 views • link

updated 13.1 years ago by dm01720 •

• written 13.1 years ago by lili •

1 answer

In /usr/local/share/perl5/Genome/Env there is a file named GENOME_DB.pm. It sets the GENOME_DB environment variable. By default, this is /var/lib/genome/db. I put the databases there and it works.

• 78 views • link

written 13.1 years ago by dm01720 •

More posts like this

Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
written 3.6 years ago by Arslan Tariq •

**Introduction** Ribosomal RNA (rRNA) genes are known to be an integral part of ribosome synthesis machinery hence been studied extensively. Due to their repetitive nature, …
Centrally installed Braker2 error: AUGUSTUS_CONFIG_PATH/species is not writeable.
written 4.0 years ago by Timotheus •

Hi, I'm trying to run Braker2 to annotate my genome with the help of RNA-seq data: ``` braker.pl \ --genome=$ASSEMBLY \ --bam=$RNA_BAM \ --gff3 \ …
Tophat Error Message
written 9.0 years ago by jammydodger123456 •

When I run a tophat job script; #!/bin/bash #$ -N TH_3hrB1 #$ -o /mnt/scratch/users/40100371/Read_Files/Mlig/3hrB1.$JOB_ID # send email when job begins end or aborts #$ -M …
Questions about using the Celera Genome Assembler for HGAP
written 10.7 years ago by tptacek3050

This post is a followup to a previous post: https://www.biostars.org/p/160935/#160938 I am trying to use the PBcR pipeline for the Celera Genome Assembler (v8.3) to …
Vcftools not running
written 11.5 years ago by pifferdavide

``` cd C:/Users/Davide/downloads #set to directory with the tabix package files tar -xf tabix-0.2.6.tar.bz2 #decompress file export PERL5LIB=/C:/Users/Davide/vcftools/perl #set the PERL5LIB environment variable to include …
Cannot Build Bio-Samtools
written 11.5 years ago by ali •

BioPerl is installed samtools 0.1.9 is used using `-fPIC` flags (I was getting `R_X_86_64_32` err). In fact I've tried adding the `-fPIC` flag and then …
MuSic Pfam file path in Linux RHEL
written 11.7 years ago by Nitish Mishra •

Hi, I am trying to use MuSic for pfam annotation on **Linux RHEL system**. I already downloaded pfam, cosmic-omim data ([genome-databases_1-1.tar.gz][1]) in my home directory …
Error In Genome Music Path-Scan
written 12.4 years ago by Andreas Weller •

I'm using Genome Music 0.4.1 on an Ubuntu 10.04 server. Most functions work fine, so I guess my installation and my input files are generally …
Genome Music Path-Scan Negative P-Value?
written 13.3 years ago by John St. John

Hello, Genome MuSic path-scan crashes with the following error on one of my datasets, and works fine with another that has identical format. Here is …
Genome Music Calc-Wig-Covg Uninitialized Error
written 13.4 years ago by NickA5133 •

I am having difficulty running this function in MuSiC. Here is the input and output returned get when I run this function: <pre><code> lailab@envy-desktop:~$ …