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nhmmer has to be 3.3.1? #7

Closed YichaoOU closed 1 year ago

YichaoOU commented 1 year ago

Hello,

I got an error in step 2 using the test data. The installation said nhmmer >= 3.3.1, and I have 3.3.2. Is it OK?

[yli11@noderome134 test_data]$ perl ../src/ESPRESSO_C.pl -I test_result -F test_data_espresso_sirv/SIRV2.fasta -X 0 -T 5
Please make sure nhmmer 3.3.1 is installed and included in $PATH! at ../src/ESPRESSO_C.pl line 135.

(captureC) [yli11@noderome134 test_data]$ echo $PATH
/hpcf/authorized_apps/rhel7_apps/hmmer/install/3.3.2/bin

(captureC) [yli11@noderome134 test_data]$ which nhmmer
/hpcf/authorized_apps/rhel7_apps/hmmer/install/3.3.2/bin/nhmmer

Thanks, Yichao

EricKutschera commented 1 year ago

The code is checking for the version to be exactly 3.3.1: https://github.com/Xinglab/espresso/blob/v1.3.0-beta/src/ESPRESSO_C.pl#L127

That is inconsistent with the README saying hmmer >= 3.3.1

I couldn't find details about what the updates are for 3.3.2 from http://hmmer.org/ but I don't know of any reason 3.3.2 should not work with ESPRESSO. For now you could comment out the line that gives the error or update the version number check in the code. I'll update at least 1 of the README or the version check in the code once I have time to test 3.3.2

YichaoOU commented 1 year ago

commented out line 129.

Thanks, Yichao

YichaoOU commented 1 year ago

Cool! I got the example all worked out!

Thanks, Yichao