Closed djakubosky closed 7 years ago
Will have to look at it.
OK. So basically that module isn't going to work anymore because it was based on the python27 RPMS that only existed in CentOS 6.
I am looking at the way the newer version of that RPM works in CentOS 7.
Thanks! This is an important library for many things I do. Appreciate the help
Understood. Its a weird method (the installation). Does this change the behavior? This is in test ONLY on fl-hn2 and note the maintainers have updated the pysam version.
$ module add python/2.7/pysam/0.11.2.2
$ python
Python 2.7.5 (default, Nov 20 2015, 02:00:19)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pysam
>>>
this actually doesn't seem to work djakubosky@fl-hn2:/frazer01/projects/CARDIPS/analysis/cardips-cnv-analysis$ module add python/2.7/pysam/0.11.2.2 ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'python/2.7/pysam/0.11.2.2'
but a problem is it actually has to be 0.8.3 to work with certain things.
many packages are very sensitive to pysam version, as I'm sure you've come to find out
You have to login/login to get the change in Modulepath I just did. Sorry.
But if 0.8.3 is required I will look into it more shortly.
I actually don't know what that means (login/login)
typo: logout/login aka exit your shell to fl-hn2 and log back in. But it won't change the 0.8.3 part. Just provide the newer one for now.
I can't exactly remember why, but that version is needed for something. I'll look back at my notes, thanks for the help!
Yeah, I've seen similar. I'm working on a compat module method for C7. Will be a bit but it should be doable.
If you happen to have a short test I can use I'm trying two paths.
fl-hn2 [~]$ module add python/2.7/pysam/0.8.3
fl-hn2 [~]$ python
Python 2.7.5 (default, Nov 20 2015, 02:00:19)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pysam
>>>
I dimly recall some pysam fragments to validate but if you have one handy.
I have no idea if that works
I will be out for a bit now but I'll keep working on it when I return. Any short validation test so I don't have to bug you would be appreciated.
Note to myself: my Cython might need an update.
Sorry. Was out of office, I'll try it out thanks!
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Note to myself: my Cython might need an update.
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Just advise when you can if the first method works and I will propagate it to the nodes. Its just on fl-hn2
right now. I will look at the generic solutions for multiple pysam versions with the same python again.
I have also made some progress with a pure build of pysam 0.8.3 on CentOS 7 compared to the copy method. So when you have time let me know if the "copy" of the old python pysam doesn't work and I can have you test this method.
I believe both methods would work but I'm trying to keep things as exactly "the same" for you as possible given the ways of pysam.
Again just to be clear: all this is ONLY on fl-hn2
for now. Not the CentOS7 nodes so test from the head node please.
seems that your copy method is functional for me, unsure if it will break when I do other tests but for now it is working.
OK. For now then I will propagate the method to the nodes via puppet. I will update this when that is done and the module works the same on all the nodes.
But once the dust clears I would like to try the fresh build when not under time pressure. Just so we don't have too many unknown methods.
Oh, and as a plus I believe my newer method would allow us to handle arbitrary pysam versions in a clean module way. I spent some time looking at the RPMs method and understand what they are doing.
OK. I believe the nodes are now consistent as well with some tests by me to verify
module add python/2.7/pysam/0.8.3
Results in the proper matching item on them. Please advise (and include node name) if you have issues!
And I believe if you did want to validate a newer pysam this also should work
module add python/2.7/pysam/0.11.2.2
No requirement you do so but preparing to support variant pysams.
Believed resolved and we also have a way to handle multiple pysams going forward. Re-open if still concerns.
module adding python/2.7/pysam/0.8.3 works on flh1 but not flh2 after CentOS6 update to CentOS7, is there something I should be doing differently?