Installing genomes from local source.

[am33567]

Hi,

I am having trouble running the script 'install_genome_data.sh'. The genome I am using is not online, it is in our lab server. I modify the script to add the genome like this:

elif [ $GENOME == "Vc" ]; then REF_FA= '~/genomes/VcPacHM_Vcq_p95_mod.fa' fi

To run the script I used: sh ./install_genome_data.sh Vc ./genome_data/

What I get is: ./install_genome_data.sh: line 137: ~/genomes/VcPacHM_Vcq_p95_mod.fa: No such file or directory

I know the file is there, if I list my file using: ls -lh ~/genomes/VcPacHM_Vcq_p95_mod.fa -rw-rw-r-- 1 am2622 am2622 406M Apr 3 13:19 /home/am2622/genomes/VcPacHM_Vcq_p95_mod.fa

Any help?

On the other hand, I have the genomes and their bowtie indexes ready, Is there a way I can indicate the pipeline the path of my files? I am not using any of the vertebrate genomes in the install_genome_data.sh' script.

Thanks,

Anyi

[leepc12]

./install_genome_data.sh cannot work without internet connection because it uses wget to download REF_FA. REF_FA should be an URL starting with http.

Please use it on the computer with internet connection and move output (built genome data) to your computer without internet.

[am33567]

Yes, but what if the genomes are not on the internet? Only on my computer?

[leepc12]

Okay let replace wget with cp. Replace line 144 (wget -c -O $(basename ${REF_FA}) ${REF_FA}) of install_genome_data.sh with the following:

cp -f ${REF_FA} .

But the installer still needs Conda environment installed on your system.

[am33567]

It worked really well.