[miso-users] miso-users Digest, Vol 66, Issue 1

Thu Oct 17 11:13:45 EDT 2019

Do you have samtools installed or loaded in your HPC environment?

Il giorno gio 17 ott 2019 alle ore 16:00 <miso-users-request at mit.edu> ha
scritto:

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> Today's Topics:
>
>    1. Installing misopy (Rayhaan Ali)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 17 Oct 2019 14:00:19 +0000
> From: Rayhaan Ali <rali03 at qub.ac.uk>
> Subject: [miso-users] Installing misopy
> To: "miso-users at mit.edu" <miso-users at mit.edu>
> Message-ID:
>         <
> DB7PR07MB59617CD7422397F7128FE962956D0 at 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.
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