FORUMGenome installation
dudemain asked 5 months ago



Hello, I\’ve been trying to install a new bovine genome assembly (ARS-UCD1.2/bosTau9) so I can get access from the mammouth server (mp2b), but I\’m running into an error when trying to copy the file /cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-3.1.4/resources/genomes/GENOME_INSTALL_TEMPLATE.sh to /cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-3.1.4/resources/genomes/Bos_taurus.bosTau9.sh. The error is cp: cannot create regular file \’/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-3.1.4/resources/genomes/Bos_taurus.bosTau9.sh\’: File exists. However the file doesn\’t already exist and I\’ve been reading a bit on forums and many people are having that kind of problem on servers. Some mention that we could need to update the spider version. Do you think that you could help me have this new bovine genome installed please? Thanks for your help

2 Answers
flefebvre Staff answered 5 months ago



Hi Pier-Luc, as Édouard replied on the C3G ticket system cross-post this morning, he will install UCSC bosTau9 or ENSEMBL ARS-UCD1.2 to the MUGQIC CVMFS for you. It should also be possible for you to install the genome in a custom location, you can ask him for specific questions on the ticket.

dudemain replied 5 months ago

Thanks for your reply, I’m not so sure what you mean by C3G ticket system, I may have further questions, but I don’t see Édouard’s answer anywhere, could you indicate me where I should go to see it? I was expecting to receive an e-mail for that ticket opening, however I didn’t get any, this is why I asked my question here too!
Sorry for the duplication!

Thanks for your help

flefebvre Staff answered 5 months ago



Hi Pier-Luc, it seems like you also posted a question in one of the forms at c3g.ca. Below is Édouard’s reply. I think the installation will be visible in CVMFS by the end of today.

Hi Pier-Luc,
This error message is surprising as CVMFS is a read-only file system…
I would have expected this kind of error instead :

cp: cannot create regular file ‘/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-3.1.4/resources/genomes/Bos_taurus.bosTau9.sh’: Read-only file system`

You can still try to use our scripts to install genomes in a custom location.
But know that I will take care of installating the BosTau9 genome in CVMFS.
Regards,
Edouard