Anaconda and Conda Env Part 2#3337
Conversation
|
Normally I love dropbox, but not being case sensitive is just aggravating. |
rework Anaconda easyconfigs based on changes to Anaconda easyblock
|
|
||
| easyblock = 'EB_CondaCreate' | ||
|
|
||
| name = "condacreate-module" |
There was a problem hiding this comment.
@jerowe I think the name used here should better reflect what is actually being installed...
This should probably be named cpanminus instead?
Does conda support providing a specific version in the requirements? Since as it is now, you have no control over which cpanminus version gets installed (and hence the version field can't be filled in meaningfully)...
There was a problem hiding this comment.
This is done in conda with perl-app-cpanminus=1.7039. Or your version number of choice. For larger modules I am very specific with version choices, but for small one off and/or dev environments I'm not. This does not seem to be the easybuild way, but I will bend to your will on this one. ;-)
I was thinking this is a general case to use conda create to create a module. What is being installed does not matter so much as the concept, but we can change it.
There was a problem hiding this comment.
That's indeed my main concern, sticking to the EasyBuild way in the central repo. Of course you can leverage the functionality as you please using your own set of easyconfigs. :)
The example easyconfig(s) we include here to use the Conda generic easyblock (which we're working towards, I think) should preferably be strict w.r.t. versions, and reflect well what can be done with the Conda easyblock...
Also, I would probably include -Anaconda2-4.0.0 as a versionsuffix, to make it clear that the installation is done on top of Anaconda (and which version of Anaconda), so it can be distinguished from a compile-from-source installation with a particular toolchain, as is usually done with EasyBuild.
| #sources = ["environment.yml"] | ||
| #environment_file = sources[0] | ||
|
|
||
| #remote_environment = "nyuad-cgsb/gencore_variant_detection_1.0" |
|
|
||
| #Use one of the following - either an environment.yml file or a remote environment definition | ||
| #sources = ["environment.yml"] | ||
| #environment_file = sources[0] |
There was a problem hiding this comment.
@jerowe this should change so that only the last line is needed; the Conda easyblock should just copy environment_file in the right location by itself?
There was a problem hiding this comment.
Actually, no change is needed at all, the requirement is just that environment_file points to the absolute path of the file, otherwise it won't be found.
| version = "1.7039" | ||
| variant = "Linux-x86_64" | ||
|
|
||
| homepage = "http://search.cpan.org/~miyagawa/Menlo-1.9003/script/cpanm-menlo" |
There was a problem hiding this comment.
maybe https://github.com/miyagawa/cpanminus is a better link?
use 'Conda' easyblock + empty version for dummy toolchain + some minor enhancements
|
|
||
| builddependencies = [('Anaconda3', '4.0.0')] | ||
|
|
||
| preinstallopts = "conda install -f -c conda conda-env=2.5.2 && " |
There was a problem hiding this comment.
its not there on mine..
ETA - I was looking at the wrong config. I removed it from gencore.
prefix 'conda install' post install command with update to $PATH so conda is found
specify installation directory in postinstallcmd
install conda 4.2.12 rather than coda-env 2.5.2 in postinstallcmds
|
Test report by @boegel |
|
Test report by @boegel |
fix directory name for perl-app-cpanminus easyconfigs
|
Tested on top of easybuilders/easybuild-easyblocks#950, all good to go, thanks @jerowe! |
I had merge conflicts and accidently deleted things:
Here is the original conversation: #3173
Sorry for the confusion!
edit: depends on easybuilders/easybuild-easyblocks#950