[miso-users] Installing misopy

[Rayhaan Ali]

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-0001.html