<html dir="ltr" style="background-image: none; background-position: 0% 0%; background-repeat: repeat repeat;">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" id="owaParaStyle">
<!--
-->
</style>
<title></title>
</head>
<body fpstyle="1" ocsi="0">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">
<div>Hello,</div>
<div>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.</div>
<div>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".</div>
<div>Does anyone knows other ways to install miso?</div>
<div>Thanks</div>
<div>Delong</div>
<div><br>
</div>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF435043" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>De :</b> miso-users-bounces@mit.edu [miso-users-bounces@mit.edu] de la part de Delong, Zhou [Delong.Zhou@usherbrooke.ca]<br>
<b>Envoyé :</b> 7 avril 2014 17:24<br>
<b>À :</b> <miso-users@mit.edu><br>
<b>Objet :</b> [miso-users] Error installing miso<br>
</font><br>
</div>
<div></div>
<div>
<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hello,
<div>I have recently removed miso and tried to reinstall miso under ubuntu, but here is the problem I have:</div>
<div><br>
</div>
<div>I used easy_install misopy to install miso. All went well. </div>
<div>import misopy and import pysplicing ok.</div>
<div>module_availability checked ok, all modules available.</div>
<div>test_miso failed with errors (see further)</div>
<div>Typing sam_to_bam or miso into the command line<span style="font-size:10pt"> </span><span style="font-size:10pt">failed</span><span style="font-size:10pt"> (command not found)</span></div>
<div>Typing index_gff works (requesting index files etc)</div>
<div><br>
</div>
<div>Does anyone know what I should do please?</div>
<div><br>
</div>
<div>Thanks</div>
<div>Delong</div>
<div><br>
</div>
<div><br>
</div>
<div><span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">Testing fr-unstranded...</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">Checking read f_read against +</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">Checking read f_read against -</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">Checking read r_read against +</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">Checking read r_read against -</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">Testing fr-firststrand...</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">Testing fr-secondstrand...</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">.Testing conversion of SAM to BAM...</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">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</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">sh: 1: sam_to_bam: not found</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">FTesting gene-level Psi...</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">Testing GFF indexing of: /home/delong/misopy-0.5.2/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">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</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">sh: 1: index_gff: not found</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">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 </span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">sh: 1: miso: not found</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">.</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">======================================================================</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">FAIL: test_a_sam_to_bam (__main__.TestMISO)</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">----------------------------------------------------------------------</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">Traceback (most recent call last):</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)"> File "misopy-0.5.2/misopy/test_miso.py", line
51, in test_a_sam_to_bam</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)"> "c2c12.Atp2b1.sorted.bam")))</span><br style="line-height:21.299999237060547px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; background-color:rgb(255,255,255)">
<span style="color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15.199999809265137px; line-height:21.299999237060547px; background-color:rgb(255,255,255)">AssertionError</span></div>
<div><br>
</div>
</div>
</div>
</div>
</div>
</body>
</html>