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Hi All, </div>
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I have been attempting to install misopy (<a href="https://miso.readthedocs.io/en/fastmiso/#" id="LPlnk184667">https://miso.readthedocs.io/en/fastmiso/#</a>) but have so far been unsuccessful. Recently, I contacted the HPC Support group at the institution
I work at.</div>
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The steps we both performed for installing misopy are:</div>
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Adding the module: apps/pip/9.0.1/python-2.7.8</div>
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<span style="color: rgb(0, 0, 0); font-family: "Segoe UI", "Helvetica Neue", sans-serif; font-size: 10pt;">Then running: pip install misopy </span><br>
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<span style="color: rgb(0, 0, 0); font-family: "Segoe UI", "Helvetica Neue", sans-serif; font-size: 10pt;">I then checked that the following directory was in my pythonpath: /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages</span></div>
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<span style="color: rgb(0, 0, 0); font-family: "Segoe UI", "Helvetica Neue", sans-serif; font-size: 10pt;"><br>
</span></div>
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<span style="color: rgb(0, 0, 0); font-family: "Segoe UI", "Helvetica Neue", sans-serif; font-size: 10pt;">This all worked fine.</span></div>
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<span style="color: rgb(0, 0, 0); font-family: "Segoe UI", "Helvetica Neue", sans-serif; font-size: 10pt;"><br>
</span></div>
<div style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; font-size: 10pt; color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0); font-family: "Segoe UI", "Helvetica Neue", sans-serif; font-size: 10pt;"><span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">To then</span><span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important"> test
the installation, in Python I did: </span></span></div>
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</span></span></div>
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<span style="color: rgb(0, 0, 0); font-family: "Segoe UI", "Helvetica Neue", sans-serif; font-size: 10pt;"><span>import misopy<br>
</span><span>import pysplicing</span></span></div>
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<span style="color: rgb(0, 0, 0); font-family: "Segoe UI", "Helvetica Neue", sans-serif; font-size: 10pt;"><span><br>
</span></span></div>
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<span style="color: rgb(0, 0, 0); font-family: "Segoe UI", "Helvetica Neue", sans-serif; font-size: 10pt;"><span>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).</span></span></div>
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</span></span></div>
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I then ran the below to test if MISO could be run:</div>
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python -m unittest discover misopy<br>
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<br>
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<span>However, I get a failure:</span></div>
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<div>Testing fr-unstranded...<br>
</div>
<div>Checking read f_read against +<br>
</div>
<div>Checking read f_read against -<br>
</div>
<div>Checking read r_read against +<br>
</div>
<div>Checking read r_read against -<br>
</div>
<div>Testing fr-firststrand...<br>
</div>
<div>.Testing conversion of SAM to BAM...<br>
</div>
<div>Executing: sam_to_bam --convert /users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam
/users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/sam-output<br>
</div>
<div>sh: sam_to_bam: command not found<br>
</div>
<div>FTesting gene-level Psi...<br>
</div>
<div>Testing GFF indexing of: /users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff<br>
</div>
<div>Executing: index_gff --index /users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
/users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed<br>
</div>
<div>sh: index_gff: command not found<br>
</div>
<div>Executing: miso --run /users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed
/users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
--output-dir /users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/gene-psi-output
--read-len 36<br>
</div>
<div>sh: miso: command not found<br>
</div>
<div>.Testing gene-level Psi...<br>
</div>
<div>Executing: python /users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/index_gff.py
--index /users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
/users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed<br>
</div>
<div>Traceback (most recent call last):<br>
</div>
<div>File "/users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/index_gff.py", line 199,
in module<br>
</div>
<div>main()<br>
</div>
<div>File "/users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/index_gff.py", line 188,
in main<br>
</div>
<div>os.makedirs(output_dir)<br>
</div>
<div>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<br>
</div>
<div>mkdir(name, mode)<br>
</div>
<div>OSError: [Errno 13] Permission denied: '/users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed'<br>
</div>
<div>Executing: python /users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/run_events_analysis.py
--compute-genes-psi /users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">12234567</span>8/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed
/users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
--output-dir /users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/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<br>
</div>
<div>MISO (Mixture of Isoforms model)<br>
</div>
<div>To run MISO, please use "miso" instead.<br>
</div>
<div>.Testing single-end SE event interface...<br>
</div>
<div>Executing: python /users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/run_events_analysis.py
--compute-events-psi se-sample /users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-data/se-counts/se_test.counts
--output-dir /users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/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<br>
</div>
<div>MISO (Mixture of Isoforms model)<br>
</div>
<div>To run MISO, please use "miso" instead.<br>
</div>
<div>.<br>
</div>
<div>======================================================================<br>
</div>
<div>FAIL: test_a_sam_to_bam (misopy.test_miso.TestMISO)<br>
</div>
<div>----------------------------------------------------------------------<br>
</div>
<div>Traceback (most recent call last):<br>
</div>
<div>File "/users/<span style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255); display: inline !important">122345678</span>/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test_miso.py", line 51, in
test_a_sam_to_bam<br>
</div>
<div>"c2c12.Atp2b1.sorted.bam")))<br>
</div>
<div>AssertionError<br>
</div>
<div><br>
</div>
<div>----------------------------------------------------------------------<br>
</div>
<div>Ran 5 tests in 2.761s<br>
</div>
<div><br>
</div>
<div>FAILED (failures=1)<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>When I do:</div>
<div>python -m unittest discover miso<br>
</div>
<div><br>
</div>
<div>I get:</div>
<div><br>
</div>
<div><span>Traceback (most recent call last):<br>
</span>
<div> 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<br>
</div>
<div> "__main__", fname, loader, pkg_name)<br>
</div>
<div> 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<br>
</div>
<div> exec code in run_globals<br>
</div>
<div> 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><br>
</div>
<div> main(module=None)<br>
</div>
<div> 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__<br>
</div>
<div> self.parseArgs(argv)<br>
</div>
<div> 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<br>
</div>
<div> self._do_discovery(argv[2:])<br>
</div>
<div> 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<br>
</div>
<div> self.test = loader.discover(start_dir, pattern, top_level_dir)<br>
</div>
<div> 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<br>
</div>
<div> raise ImportError('Start directory is not importable: %r' % start_dir)<br>
</div>
<span>ImportError: Start directory is not importable: 'miso'</span><br>
</div>
<div><br>
</div>
<span>
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<span><br>
</span></div>
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<span><br>
</span></div>
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. </span><br>
</div>
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<span><br>
</span></div>
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<span>Is anyone able to help with this? I would be grateful for any advice.</span></div>
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<span><br>
</span></div>
<div style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; font-size: 10pt; color: rgb(0, 0, 0);">
<span>Thanks,</span></div>
<div style="font-family: "Segoe UI", "Helvetica Neue", sans-serif; font-size: 10pt; color: rgb(0, 0, 0);">
<span>Ali.</span></div>
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