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Transipedia / dekupl-run

Identify differentially expressed k-mers between RNA-Seq datasets
MIT License
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Gencode data has moved #50

Closed amirkdv closed 5 years ago

amirkdv commented 5 years ago

Gencode data is no longer hosted at ftp://ftp.sanger.ac.uk/pub/gencode/:

$ curl ftp://ftp.sanger.ac.uk/pub/gencode/README.txt
The GENCODE data can now be found at
ftp://ftp.ebi.ac.uk/pub/databases/gencode/

As it stands we get the following error:

Connecting to ftp.sanger.ac.uk (ftp.sanger.ac.uk)|193.62.203.115|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/gencode/Gencode_human/release_24 ...
No such directory ‘pub/gencode/Gencode_human/release_24’.

[Thu Nov 15 00:12:15 2018]
Error in rule gencode_download:
    jobid: 10
    output: results/references/gencode.v24.transcripts.fa.gz

Pull request to fix will be submitted shortly.

jaudoux commented 5 years ago

@amirkdv Docker and Conda are up to date with the last release integration your patch.

Best, J.

amirkdv commented 5 years ago

Thank you @jaudoux