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ntm / grexome-TIMC-Secondary

exome pipeline from TIMC - secondary analyses (GVCF to analysis-ready TSVs)
GNU General Public License v3.0
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generate updated list of canonical transcripts #3

Closed Chris-lang478 closed 2 years ago

Chris-lang478 commented 2 years ago

@ntm Nicolas, Thanks again for your great work. I was trying to generate updated list of canonical transcripts follow your scripts. However, I met ERROR 2003 (HY000): Can't connect to MySQL server on 'ensembldb.ensembl.org:3306' (110). I am new to Linux system, I have tried google for the solution, but I just can't figure it out. And I don't have root access. Could you offer more details for 'Just run it from eg nicofree'? Or could you offer the listCanonicalTranscripts_22017.tsv.gz? Thanks again for your help!

Best regards, Chris

ntm commented 2 years ago

Hi @Chris-lang478 , I suspect the issue here is that listCanonicalTranscripts_MYSQL.sh connects to the public Ensembl MySQL server, on port TCP/3306. Unfortunately, outgoing traffic to this port is sometimes blocked by your institutional firewall - this is the case where I work, and being root on your system wouldn't help. As a workaround, I run that script from my home computer (called nicofree): this works fine, my ISP at home doesn't filter outgoing traffic. You could do the same, but I'm just attaching the latest version for you: listCanonicalTranscripts_220717.tsv.gz Cheers, Nicolas

ntm commented 2 years ago

I see in another issue that my resolution solved this, closing