Trinity: need to remove @ from paths in perl script

[bernt-matthias]

Happens within Galaxy which uses the @ character in the environment names.

Error is:

Possible unintended interpolation of @2 in string at /gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda/envs/__trinity@2.8.4/bin/Trinity line 46.

Had the same problem in the stacks2 wrapper. For variables setting path to binaries that are on the PATH anyway the solution is to set them to an empty string.

For the others (like paths to jar files), a fix might involve using some pwd magic.

[epruesse]

Is this a Bioconda issue (packaging) or an upstream problem at Trinity (software)?

ping @bgruening - if this is galaxy specific, maybe you know who could help.

[bernt-matthias]

Kind of both: The cause of the problem is that galaxy uses an @ character in the environment names (__name@version).

If perl packages/programs use hard coded paths (e.g. via an install script that uses BIN_DIR as parameter) for dependencies, then the perl interpreter has problems in this case since the @ should be quoted.

One solution is to remove the hard coded paths (which I did for stacks) since the binaries are on the PATH anyway. Alternatively the @ could be quoted. Don't know if conda could do this in general for BIN_DIR (or all its path).

[epruesse]

So basically, you are saying that Trinity's perl code breaks if Trinity is installed into a directory that has an @ in it? That sounds like something that needs to be fixed in Trinity. Galaxy is doing something unusual, but nothing wrong. Neither is Conda when it rewrites the paths. How does the proper Perl Quoting look like? It might be something to add to conda - rewrite the strings with correct quoting if it's a perl file.

[bernt-matthias]

I'm no perl expert, but \@ should do the trick.

[epruesse]

@msarahan Can you pitch in with suggestions here?

From bin/Trinity:

#!/usr/bin/env perl
[...]
my $TRIMMOMATIC = "/opt/anaconda1anaconda2anaconda3/share/trimmomatic/trimmomatic.jar";

So installing into an env with $ or @ in it breaks the script during path rewriting.

Do you have code handling this for bash? Is there a chance to add code to conda to escape the @ for perl files?

[msarahan]

no, I don't think we have anything for that currently. A PR to add it would be welcome.

[epruesse]

Quick pointer where it would have to go? (term that can be grepped suffices)

[epruesse]

@bernt-matthias For the time being, can you come up with a patch for Trinity? Using ' instead of " should suffice for the variables in question. A PR against conda would fix this for good, but take quite a while until it has arrived at everyone's desks.

[epruesse]

(Or use q[text] or q{text} or q(text) instead. Perl has a veritable arsenal of ways to write a string constant)

[epruesse]

I've created an issue for now (conda/conda#8601), adding to the nearly 1k open ones over there.

[bernt-matthias]

done #14741