ENH: ssu-align

[wasade]

Need to set $SSUALIGNDIR in build.sh, so I do not expect this to pass yet. make check does not pass out of the box on my laptop due to a missing perl dependency (details below).

$ make check
...snip...
Running Easel test suite...

Can't locate getopts.pl in @INC (@INC contains: /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at ./../devkit/sqc line 208.
make[2]: *** [run_sqc] Error 2
make[1]: *** [check] Error 2
make: *** [check] Error 2

[wasade]

I think this is there for Linux. The tests (i.e., make check) don't seem to run on OSX unfortunately.

[colinbrislawn]

The issue is that Easel calls getopts.pl which is not part of the newer Perl that OSX uses. Solution is for getopts.pl to be updated to use the replcament command, or newer verions of Easel to be used. Unfortunately, ssu-align is not on github and not under active development so this is kind of a mess.

However, Infernal and Easel and their developers are on github!
Hey @cryptogenomicon, we love your software. Any guidance here?

@wasade How are we using ssu-align anyway? (Sorry if this is dumb question.)

[wasade]

Greengenes and EMP right now, and @gregcaporaso has been using it but i
don't know for what specifically off hand. I also don't believe ssu-align
is being maintained anymore, so beyond installation issues, we won't be
able to readily take advantage of Infernal improvements.

Cc @nawrockie
On Feb 13, 2016 11:35 PM, "Colin Brislawn" notifications@github.com wrote:

The issue is that Easel calls getopts.pl which is not part of the newer
Perl that OSX uses. Solution is for getopts.pl to be updated to use the
replcament command, or newer verions of Easel to be used. Unfortunately,
ssu-align is not on github and not under active development so this is kind
of a mess.

However, Infernal and Easel and their developers are on github!
Hey @cryptogenomicon https://github.com/cryptogenomicon, we love your
software. Any guidance here?

@wasade https://github.com/wasade How are we using ssu-align anyway?
(Sorry if this is dumb question.)

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#44 (comment).

[nawrockie]

Changes to a few lines of a single file in Easel (ssu-align-0.1/infernal/easel/devkit/sqc) will sidestep the getopts.pl issue. I have that patch if you'd like it.

[colinbrislawn]

Thanks for the patch. But where should we put it?

Maybe we could rehost the original ssu-align-0.1 code on github as part of biocore. Input from @cryptogenomicon and @elena-rivas would be really helpful because this code came out of their lab.

[cryptogenomicon]

Eric Nawrocki, who sent you the patch, is the lead developer of Infernal and ssu-align.

On Feb 14, 2016, at 4:40 PM, Colin Brislawn notifications@github.com wrote:

Thanks for the patch. But where should we put it?

Maybe we could rehost the original ssu-align-0.1 code on github as part of biocore. Input from @cryptogenomicon and @elena-rivas would be really helpful because this code came out of their lab.

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[colinbrislawn]

Oh I had no idea. Thanks for helping us out with this! @nawrockie, how can we best incorporate your patch?

[nawrockie]

We are working on putting ssu-align on github, I'll write again when that's happened.

[colinbrislawn]

Thanks Eric. The Biocore folks make good use of this software and we appreciate the patch.

[wasade]

Thanks, Eric!
On Feb 15, 2016 11:42 PM, "Colin Brislawn" notifications@github.com wrote:

Thanks Eric. The Biocore folks make good use of this software and we
appreciate the patch.

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#44 (comment).

[nawrockie]

We've got ssu-align on github, and I am going to start working on a 0.1.1 release including the Easel getopts.pl bug fix today. I'm not sure how long it will take.

[colinbrislawn]

Thanks for helping us out with this!

I'm sorry I overlooked the ssu-align github repo: https://github.com/EddyRivasLab/ssu-align

[nawrockie]

I'm sorry I overlooked the ssu-align github repo: https://github.com/EddyRivasLab/ssu-align

You didn't, we just created it yesterday.

[nawrockie]

There's now a new version of ssu-align (0.1.1) available for download here:
http://eddylab.org/software/ssu-align/ssu-align-0.1.1.tar.gz

The 'make test' error you reported and some other bugs are fixed in 0.1.1, but there are not any other substantial changes to the software.

[wasade]

Great, thank you!

On Wed, Feb 24, 2016 at 5:40 AM, Eric Nawrocki notifications@github.com
wrote:

There's now a new version of ssu-align (0.1.1) available for download here:
http://eddylab.org/software/ssu-align/ssu-align-0.1.1.tar.gz

The 'make test' error you reported and some other bugs are fixed in 0.1.1,
but there are not any other substantial changes to the software.

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#44 (comment).

[nawrockie]

You're welcome, thanks for using our software.

[wasade]

@colinbrislawn, when you have a moment, could you take a look at the failure here? One build is failing, and the other is passing, but I'm not familiar enough with the build system in this repo to know what the differences are between the two builds.

[colinbrislawn]

The error is
Can't locate getopts.pl in @INC...
It's one I've run into before when trying perl builds on OSX. Apparently there is a simple fix.
https://unix.stackexchange.com/questions/224716/perl-library-getopts-pl

I'm pretty swamped right now. It's going to be awhile before I can make a PR. You want this one?

[nawrockie]

Are you guys using the new version 0.1.1? That error shouldn't occur with 0.1.1.

[http://eddylab.org/software/ssu-align/ssu-align-0.1.1.tar.gz]

[wasade]

oh, hah! Thanks @nawrockie. Will update.

And thanks @colinbrislawn

[wasade]

Well, the new error does appear to be from the repo itself