Do you have samtools installed or loaded in your HPC environment? Il giorno gio 17 ott 2019 alle ore 16:00 <[email protected]> ha scritto:
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Installing misopy (Rayhaan Ali) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Oct 2019 14:00:19 +0000 > From: Rayhaan Ali <[email protected]> > Subject: [miso-users] Installing misopy > To: "[email protected]" <[email protected]> > Message-ID: > < > db7pr07mb59617cd7422397f7128fe96295...@db7pr07mb5961.eurprd07.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi All, > > I have been attempting to install misopy ( > https://miso.readthedocs.io/en/fastmiso/#) but have so far been > unsuccessful. Recently, I contacted the HPC Support group at the > institution I work at. > > The steps we both performed for installing misopy are: > > Adding the module: apps/pip/9.0.1/python-2.7.8 > Then running: pip install misopy > I then checked that the following directory was in my pythonpath: > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages > > This all worked fine. > > To then test the installation, in Python I did: > > import misopy > import pysplicing > > This all worked without outputting an error (previously, when I was first > installing misopy I was creating a virtual env etc. but getting an error > with 'import pysplicing'. HPC Support then suggested the above method for > installing). > > I then ran the below to test if MISO could be run: > > python -m unittest discover misopy > > However, I get a failure: > > Testing fr-unstranded... > Checking read f_read against + > Checking read f_read against - > Checking read r_read against + > Checking read r_read against - > Testing fr-firststrand... > .Testing conversion of SAM to BAM... > Executing: sam_to_bam --convert > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/sam-output > sh: sam_to_bam: command not found > FTesting gene-level Psi... > Testing GFF indexing of: > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff > Executing: index_gff --index > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed > sh: index_gff: command not found > Executing: miso --run > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam > --output-dir > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/gene-psi-output > --read-len 36 > sh: miso: command not found > .Testing gene-level Psi... > Executing: python > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/index_gff.py > --index > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed > Traceback (most recent call last): > File > "/users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/index_gff.py", > line 199, in module > main() > File > "/users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/index_gff.py", > line 188, in main > os.makedirs(output_dir) > File > "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/os.py", > line 157, in makedirs > mkdir(name, mode) > OSError: [Errno 13] Permission denied: > '/users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed' > Executing: python > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/run_events_analysis.py > --compute-genes-psi > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam > --output-dir > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/gene-psi-output > --read-len 36 --paired-end 250 30 --use-cluster > MISO (Mixture of Isoforms model) > To run MISO, please use "miso" instead. > .Testing single-end SE event interface... > Executing: python > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/run_events_analysis.py > --compute-events-psi se-sample > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-data/se-counts/se_test.counts > --output-dir > /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/SE-output > --read-len 35 --overhang-len 4 --event-type SE --use-cluster > MISO (Mixture of Isoforms model) > To run MISO, please use "miso" instead. > . > ====================================================================== > FAIL: test_a_sam_to_bam (misopy.test_miso.TestMISO) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test_miso.py", > line 51, in test_a_sam_to_bam > "c2c12.Atp2b1.sorted.bam"))) > AssertionError > > ---------------------------------------------------------------------- > Ran 5 tests in 2.761s > > FAILED (failures=1) > > > When I do: > python -m unittest discover miso > > I get: > > Traceback (most recent call last): > File > "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/runpy.py", > line 162, in _run_module_as_main > "__main__", fname, loader, pkg_name) > File > "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/runpy.py", > line 72, in _run_code > exec code in run_globals > File > "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/unittest/__main__.py", > line 12, in <module> > main(module=None) > File > "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/unittest/main.py", > line 94, in __init__ > self.parseArgs(argv) > File > "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/unittest/main.py", > line 113, in parseArgs > self._do_discovery(argv[2:]) > File > "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/unittest/main.py", > line 214, in _do_discovery > self.test = loader.discover(start_dir, pattern, top_level_dir) > File > "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/unittest/loader.py", > line 204, in discover > raise ImportError('Start directory is not importable: %r' % start_dir) > ImportError: Start directory is not importable: 'miso' > > > > It looks like the commands for running Miso are not being recognised? > I've checked the dependancy packages needed for Miso to run without a > failure, and they satisfy the requirements in terms of versions. > miso/misopy are not recognised either in Python or outside of python. > > Is anyone able to help with this? I would be grateful for any advice. > > Thanks, > Ali. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mailman.mit.edu/pipermail/miso-users/attachments/20191017/b7420ebb/attachment.html > > ------------------------------ > > _______________________________________________ > miso-users mailing list > [email protected] > http://mailman.mit.edu/mailman/listinfo/miso-users > > > End of miso-users Digest, Vol 66, Issue 1 > ***************************************** >
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