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bluegenes / MakeMyTranscriptome

assemble, annotate, and assess transcriptomes in a single step
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Manage db -- PFAM #4

Closed bluegenes closed 8 years ago

bluegenes commented 8 years ago

Add PFAM db download: wget https://data.broadinstitute.org/Trinity/Trinotate_v2.0_RESOURCES/Pfam-A.hmm.gz gunzip Pfam-A.hmm.gz hmmpress Pfam-A.hmm

bluegenes commented 8 years ago

let's change the link to the PFAM (not trinotate) source: ftp://ftp.ebi.ac.uk/pub/databases/Pfam//releases/Pfam28.0/Pfam-A.hmm.gz

bluegenes commented 8 years ago

Manage DB failed at this step: getting https://data.broadinstitute.org/Trinity/Trinotate_v2.0_RESOURCES/Pfam-A.hmm.gz Traceback (most recent call last): File "manage_database.py", line 201, in main() File "manage_database.py", line 186, in main log_table = download_databases(log_table) File "manage_database.py", line 150, in download_databases partial_get('gz', url_pfam_db, pfam_db_target) File "manage_database.py", line 140, in partial_get = lambda a, b, c: get(log_table, a, b, c) File "manage_database.py", line 123, in get print('failed to install {0!s}'.format(basename(arget))) UnboundLocalError: local variable 'basename' referenced before assignment ^C [1]+ Exit 1 python manage_database.py