{tools}[dummy/dummy] hub 2.2.2 (REVIEW) by nathanhaigh · Pull Request #2249 · easybuilders/easybuild-easyconfigs

nathanhaigh · 2016-01-04T03:52:35Z

Easyconfig for installing hub 2.2.2.

hpcugentbot · 2016-01-04T03:52:36Z

Automatic reply from Jenkins: Can I test this?

boegel · 2016-01-04T09:19:50Z

maybe change this to:

source_urls = ['https://github.com/github/hub/releases/download/v%(version)s/'] sources = ['%(namelower)s%(versionsuffix)s-%(version)s.tgz']

boegel · 2016-01-04T09:21:55Z

@nathanhaigh: have you tried building it from source? We already have easyconfigs for Go, so may be easy?

boegel · 2016-01-04T09:22:03Z

Jenkins: ok to test

hpcugentbot · 2016-01-04T09:55:17Z

Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/5397/console for more details).

This pull request is now ready for review/testing.

Please try and find someone who can tackle this; contact @boegel if you're not sure what to do.

nathanhaigh · 2016-01-04T12:22:43Z

I did try building from source, but hub recommends using the binaries. I haven't any experience with Go and only marginally more with EasyBuild! I wasn't sure what EasyBlock to use and if there are existing tools using it which I could learn from.

Happy to submit a PR for an easyconfig building from source if I can get a bit of guidance.

hpcugentbot · 2016-01-04T22:43:57Z

Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/5400/console for more details).

This pull request is now ready for review/testing.

Please try and find someone who can tackle this; contact @boegel if you're not sure what to do.

boegel · 2016-01-05T08:50:24Z

@nathanhaigh: ok, no problem, it's just that we try to stay away from binary packages when we can (not sure if it matters a lot for tools written in Go though); let's follow this up in the issue you opened (#2251)

boegel · 2016-01-05T08:51:19Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
Linux SL 6.7, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/15f2a858b0445acb9e55 for a full test report.

boegel · 2016-01-05T09:09:35Z

Going in, thanks @nathanhaigh!

nathanhaigh · 2016-01-06T02:53:21Z

Hold off merging this for the moment. I'm experiencing some odd behaviour once I've loaded the module and then run eb to install a tool.

What I've noticed is that during the configuring step of eb blah.eb I get 10's of thousands of hub processes being spawned.

nathanhaigh · 2016-01-06T03:14:34Z

This is what module show ouputs:

$ module show hub/2.2.2-linux-amd64
-------------------------------------------------------------------------------------------------------------------------
   /mnt/bioinf-7/easybuild/modules/tools/hub/2.2.2-linux-amd64:
-------------------------------------------------------------------------------------------------------------------------
whatis("Description: hub is a command-line wrapper for git that makes you better at GitHub. - Homepage: https://hub.github.co
m/ ")
conflict("hub")
prepend_path("MANPATH","/opt/shared_apps/easybuild/software/hub/2.2.2-linux-amd64/share/man")
prepend_path("PATH","/opt/shared_apps/easybuild/software/hub/2.2.2-linux-amd64/bin")
setenv("EBROOTHUB","/opt/shared_apps/easybuild/software/hub/2.2.2-linux-amd64")
setenv("EBVERSIONHUB","2.2.2")
setenv("EBDEVELHUB","/opt/shared_apps/easybuild/software/hub/2.2.2-linux-amd64/easybuild/hub-2.2.2-linux-amd64-easybuild-deve
l")
prepend_path("PATH","/opt/shared_apps/easybuild/software/hub/2.2.2-linux-amd64")
help([[ hub is a command-line wrapper for git that makes you better at GitHub. - Homepage: https://hub.github.com/

]])

Notice that last prepend_path adds /opt/shared_apps/easybuild/software/hub/2.2.2-linux-amd64 to the PATH. Well, in that directory is an executable called install which is confusing eb during the configuring step. I don't think this should be added to the path.

Other than the hub binary under the bin directory, there is also man pages under share and some auto-completion config files under etc:

$ ls -1 /opt/shared_apps/easybuild/software/hub/2.2.2-linux-amd64
bin
easybuild
etc
install
LICENSE
README.md
share

So I'm wondering how best to deal with all of these things.

boegel · 2016-01-06T07:03:32Z

Hmm, for some reason I ended up not hitting the merge button on this on yet, even though I intended to.

The problem you ran into is indeed worrying.

It's caused by the Binary easyblock (from which the PackedBinary used here) also considering '' (a path relative to the install directory) for $PATH. It probably shouldn't be doing that blindly, but conditionally, so we can make sure the install dir is not prepended to $PATH in this case?

nathanhaigh · 2016-01-06T20:55:07Z

The reason this is so bad is that the install script provided by hub actually calls install which it expects on the PATH. Since the install provided by hub is on the PATH, we get recursive calls, ugh!

Not adding the install dir to PATH would work - can you make those changes @boegel?

nathanhaigh · 2016-01-10T23:31:56Z

Damn, deleted my branch by mistake - restored it now :)

hpcugentbot · 2016-01-10T23:31:59Z

Automatic reply from Jenkins: Can I test this?

hpcugentbot · 2016-01-10T23:32:00Z

Automatic reply from Jenkins: Can I test this?

This avoids issues with the `installdir` being unconditionally added to the PATH by the module.

nathanhaigh · 2016-01-11T01:07:36Z

@boegel the latest commit addresses these issues without the need to modify what gets prepended to PATH. Although the latter would be a better solution, at least this easyconfig won't cause these issues now.

boegel · 2016-01-11T06:54:50Z

Jenkins: ok to test

boegel · 2016-01-11T06:55:26Z

hmm, are you sure this is OK? Why is this script there at all?

Yep, here's more info easybuilders/easybuild-easyblocks#801

The actual install script provided by hub can be seen here: https://github.com/github/hub/blob/master/script/install.sh. Line 22 ends up calling itself recursively because the installdir is added to the PATH.

Making the script non-executable is a workaround.

hpcugentbot · 2016-01-11T07:25:52Z

Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/5583/console for more details).

This pull request is now ready for review/testing.

Please try and find someone who can tackle this; contact @boegel if you're not sure what to do.

boegel · 2016-01-17T14:11:54Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
Linux SL 6.7, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/f35de541b5fe44046230 for a full test report.

boegel · 2016-01-17T14:11:59Z

lgtm

boegel · 2016-01-17T14:13:03Z

Going in, thanks @nathanhaigh!

Added hub-2.2.2

a6be6d1

boegel reviewed Jan 4, 2016
View reviewed changes

boegel added this to the v2.6.0 milestone Jan 4, 2016

Minor reformatting as suggested by @boegel

be02138

nathanhaigh mentioned this pull request Jan 4, 2016

Building a tool using Go #2251

Closed

boegel mentioned this pull request Jan 5, 2016

Easyconfig for installing hub 2.2.2 #2248

Closed

nathanhaigh changed the title ~~Added easyconfig for hub-2.2.2~~ {tools}[dummy/dummy] hub 2.2.2 (OK) Jan 5, 2016

nathanhaigh changed the title ~~{tools}[dummy/dummy] hub 2.2.2 (OK)~~ {tools}[dummy/dummy] hub 2.2.2 (WIP) Jan 6, 2016

nathanhaigh closed this Jan 10, 2016

nathanhaigh deleted the hub branch January 10, 2016 22:55

nathanhaigh restored the hub branch January 10, 2016 23:31

nathanhaigh reopened this Jan 10, 2016

Make hub's install script non-executable.

69254c1

This avoids issues with the `installdir` being unconditionally added to the PATH by the module.

nathanhaigh mentioned this pull request Jan 11, 2016

Binary unconditionaly prepends installdir to PATH easybuilders/easybuild-easyblocks#801

Closed

nathanhaigh changed the title ~~{tools}[dummy/dummy] hub 2.2.2 (WIP)~~ {tools}[dummy/dummy] hub 2.2.2 (REVIEW) Jan 11, 2016

boegel reviewed Jan 11, 2016
View reviewed changes

boegel added a commit that referenced this pull request Jan 17, 2016

Merge pull request #2249 from nathanhaigh/hub

ef7e722

boegel merged commit ef7e722 into easybuilders:develop Jan 17, 2016

nathanhaigh deleted the hub branch February 9, 2016 23:21

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