[miso-users] RE : Error installing miso

[Delong, Zhou]

Hello,
Sorry to bring up this topic again but I still have problem with this installation.. Can anyone give me some suggestion please?
Thanks
Delong


________________________________
De : Delong, Zhou
Envoyé : 17 avril 2014 12:02
À : <miso-users at mit.edu>
Objet : RE : Error installing miso

Hello,
After seeing the difference between miso 0.5.x and 0.4.x I wanted to reinstall the 0.4 version but I again failed with the problems discribed below.. Last time what I did was to reinstall everythin and it worked, but this time I tried it on a new machine but the problem still persist.
The critical point is that after easy_install or python setup.py install the system does not recognize "miso" command and I dont find any executable file named "miso".
Does anyone knows other ways to install miso?
Thanks
Delong

________________________________
De : miso-users-bounces at mit.edu [miso-users-bounces at mit.edu] de la part de Delong, Zhou [Delong.Zhou at usherbrooke.ca]
Envoyé : 7 avril 2014 17:24
À : <miso-users at mit.edu>
Objet : [miso-users] Error installing miso

Hello,
I have recently removed miso and tried to reinstall miso under ubuntu, but here is the problem I have:

I used easy_install misopy to install miso. All went well.
import misopy and import pysplicing ok.
module_availability checked ok, all modules available.
test_miso failed with errors (see further)
Typing sam_to_bam or miso into the command line failed (command not found)
Typing index_gff works (requesting index files etc)

Does anyone know what I should do please?

Thanks
Delong


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 fr-secondstrand...
.Testing conversion of SAM to BAM...
Executing: sam_to_bam --convert /home/delong/misopy-0.5.2/misopy/test-data/sam-data/c2c12.Atp2b1.sam /home/delong/misopy-0.5.2/misopy/test-output/sam-output
sh: 1: sam_to_bam: not found
FTesting gene-level Psi...
Testing GFF indexing of: /home/delong/misopy-0.5.2/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
Executing: index_gff --index /home/delong/misopy-0.5.2/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /home/delong/misopy-0.5.2/misopy/gff-events/mm9/genes/Atp2b1/indexed
sh: 1: index_gff: not found
Executing: miso --run /home/delong/misopy-0.5.2/misopy/gff-events/mm9/genes/Atp2b1/indexed /home/delong/misopy-0.5.2/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /home/delong/misopy-0.5.2/misopy/test-output/gene-psi-output --read-len 36
sh: 1: miso: not found
.
======================================================================
FAIL: test_a_sam_to_bam (__main__.TestMISO)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "misopy-0.5.2/misopy/test_miso.py", line 51, in test_a_sam_to_bam
    "c2c12.Atp2b1.sorted.bam")))
AssertionError

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