[miso-users] Error installing miso

[Delong, Zhou]

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.mit.edu/pipermail/miso-users/attachments/20140407/ba0d44ee/attachment.htm