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ogotoh / spaln

Genome mapping and spliced alignment of cDNA or amino acid sequences
GNU General Public License v2.0
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ALN_TAB? #8

Open cistarsa opened 6 years ago

cistarsa commented 6 years ago

Unable to run newest version of spaln using existing database and input:

IldModel.txt not found! Confirm whether ALN_TAB is correctly set

please advise.

pvanheus commented 5 years ago

@kingcohn1 The ALN_TAB environment variable must refer to the directory where the contents of the table directory from the spaln source is located. Similarly the ALN_DBS environment variable must refer to the directory containing seqdb from the spaln source.

jwasmuth commented 5 years ago

I installed the latest version (2.3.2) using conda and the table directory doesn't contain IldModel.txt. I cannot find the file in the 2.3.2 installation, nor an earlier installation. Any help gratefully accepted.

jwasmuth commented 5 years ago

@kingcohn1 You could copy or wget this file https://raw.githubusercontent.com/ogotoh/spaln/master/table/IldModel.txt into the table directory. Works for me.

pvanheus commented 5 years ago

@jwasmuth which search mode (i.e. -Q) parameter are you using?

jwasmuth commented 5 years ago

@pvanheus -Q7 Perhaps, I'm doing something wrong.

pvanheus commented 5 years ago

@jwasmuth nothing wrong on your side. I traced through the source code and that file is opened in the max_intron_len() function which came along with the initial code commit yet the file was only added in September 2018, i.e. after the release of spaln 2.3.2. The conda recipe should be updated to fetch it.

pvanheus commented 5 years ago

This issue is resolved by spaln release 2.3.3 (which is now available via bioconda), so this issue can be closed.