Installing netMHCpan and netMHCIIpan

[pedromachadorodri]

I'm trying to install netMHCpan and netMHCIIpan but I'm with difficulties. In the terminal shows these output 1 protein sequences /bin/sh: 1: netMHCpan: not found netmhcpan not installed

[dmnfarrell]

The command netMHCpan needs to be in your path. Did you copy the script to a location where it will be picked up like /usr/local/bin

Did you follow these instructions?

  INSTALLATION

   1. Uncompress and untar the package:

      cat netMHCpan-4.1.<unix>.tar.gz | uncompress | tar xvf -

      This will produce a directory 'netMHCpan-4.1'.

   2. From the CBS website download the file:

      https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/data.tar.gz      

      Put it in the 'netMHCpan-4.1' directory and
      then untar it:

      tar -xvf data.tar.gz

      This will produce a directory 'data'.  It is necessary  for the
      NetMHCpan 4.1 software to operate;  once it is installed you may delete
      the 'data.tar.gz' file; it will not be needed.

   2. In the 'netMHCpan-4.1' directory edit the script 'netMHCpan':

      a. At the top of the file  locate the part labelled  "GENERAL SETTINGS:
         CUSTOMIZE TO YOUR SITE"  and set  the 'NMHOME' variable  to the full
         path to the 'netMHCpan-4.1' directory on your system;

      b. Set TMPDIR to the full path to the temporary directory of you choice. It must
         be user-writable. You may for example set it to $NMHOME/tmp (and create
         the tmp folder in the netMHCpan-4.1 directory).

   3. In the 'netMHCpan-4.1/test' directory test the software:

      > ../netMHCpan -p test.pep > test.pep.myout
      > ../netMHCpan test.fsa > test.fsa.myout
      > ../netMHCpan -hlaseq B0702.fsa -p test.pep > test.pep_userMHC.myout
      > ../netMHCpan -p test.pep -BA > test.pep_BA.out
      > ../netMHCpan -p test.pep -BA -xls -a HLA-A01:01,HLA-A02:01 -xlsfile my_NetMHCpan_out.xls

      The resulting ".myout" files  should not differ  from the corresponding
      ".out" files provided in the package  other than in the directory names
      and small rounding errors.

   4. Finish the installation:

      a. Copy or link the 'netMHCpan' file to a directory in the users' path.

      b. Copy the 'netMHCpan.1' file to a location  in your manual system. If
         you need a compiled version try running:

         man -d netMHCpan.1 | compress >netMHCpan.Z

         or:

         neqn netMHCpan.1 | tbl | nroff -man | col | compress >netMHCpan.Z

[crownwang301]

the data set of BA is that the first column is peptide, the secondary column is transformed binding affinity, the third column is the class i allele. What is the fourth column?

[partrita]

In my case, after install netMHCIIpan than copy script to usr/local/bin folder.

sudo mv netMHCIIpan /usr/local/bin

It works.