Bug 258478 - biology/emboss: Add wrapper to eliminate need for altered PATH
Summary: biology/emboss: Add wrapper to eliminate need for altered PATH
Status: New
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Some People
Assignee: Wen Heping
URL:
Keywords:
Depends on:
Blocks:
 
Reported: 2021-09-13 13:43 UTC by Jason W. Bacon
Modified: 2021-09-15 13:35 UTC (History)
1 user (show)

See Also:
bugzilla: maintainer-feedback? (wen)


Attachments
Unified diff adding C wrapper (1.24 KB, patch)
2021-09-13 13:43 UTC, Jason W. Bacon
no flags Details | Diff
Improved wrapper (added usage message) (3.92 KB, patch)
2021-09-15 13:35 UTC, Jason W. Bacon
no flags Details | Diff

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Description Jason W. Bacon freebsd_committer 2021-09-13 13:43:39 UTC
Created attachment 227873 [details]
Unified diff adding C wrapper

The attached patch turns emboss commands into subcommands much like those used by bwa, samtools, bedtools, etc.  This allows users to run emboss commands without altering their PATH, and allows simultaneous access to conflicting commands such as /usr/local/bin/garnier and /usr/local/emboss/bin/garnier.

E.g.

emboss garnier   # Runs /usr/local/emboss/bin/garnier
garnier          # Runs /usr/local/bin/garnier (from biology/fasta)
Comment 1 Jason W. Bacon freebsd_committer 2021-09-13 13:44:23 UTC
Forgot to mention, I have already asked upstream to include this in future distributions.
Comment 2 Jason W. Bacon freebsd_committer 2021-09-15 13:35:24 UTC
Created attachment 227917 [details]
Improved wrapper (added usage message)