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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