netMHCIIpan-4.0的安装与使用

The NetMHCIIpan 4.0 software predicts binding of peptides to MHC class II molecules. The predictions are available for all three human MHC class II isotypes: HLA-DR, HLA-DP and HLA-DQ, as well as for mouse molecules (H-2). The method is described in detail in the following articles:

Improved prediction of MHC II antigen presentation through integration and motif deconvolution of mass spectrometry MHC eluted ligand data. Reynisson B, Barra C, Kaabinejadian S, Hildebrand WH, Peters B, Nielsen M.J. Proteome Res. 2020 Apr 18. doi: 10.1021/acs.jproteome.9b00874.

install

下载得到netMHCIIpan-4.0.Linux.tar.gz

解压：

tar zxvf netMHCIIpan-4.0.Linux.tar.gz

得到：netMHCIIpan-4.0

cd netMHCIIpan-4.0

下载：

From the CBS WWW site download the file:
https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/data.tar.gz
      Put it in the 'netMHCIIpan-4.0' directory and then gunzip and untar it:
      tar -xvf data.tar.gz
      This will produce the directory 'data'.  It is necessary for the
      NetMHCpanII 4.0 software  to  operate; once it has been  installed the
      'data.tar.gz' file may be deleted.
tar zxvf data.tar.gz

设置：

如下图：需要设置2个地方：

3\. In the 'netMHCIIpan-4.0' directory edit the script 'netMHCIIpan':
      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 'netMHCIIpan-4.0' directory on your system;
      b. Set TMPDIR to the full path to the tmp directory of you choice (must
         be user writable);

image.png

测试：

cd test/

> ../netMHCIIpan -f example.fsa -a DRB1_0101 > example.fsa.myout
> ../netMHCIIpan -f example.pep -inptype 1 -a DRB1_0101 > example.pep.myout
> ../netMHCIIpan -f example.fsa -a H-2-IAb -s -u > example.fsa.sorted.myout
> ../netMHCIIpan -f example.fsa -hlaseq DRB10101.fsa > example.fsa_hlaseq.myout
> ../netMHCIIpan -f example.fsa -hlaseqA alpha.dat -hlaseq beta.dat > example.fsa_hlaseq_A+B.myout

The resulting "*.myout" files  should be identical to the corresponding "*.out" files provided in the package.

测试报错：

$ ../netMHCIIpan -f example.fsa -a DRB1_0101 > example.fsa.myout
-bash: ../netMHCIIpan: /bin/tcsh: bad interpreter: No such file or directory

安装 tcsh：
sudo apt install tcsh

完成后重新测试。
全部没有报错。
安装成功：

将路径链接到/usr/local/bin/目录下：

sudo ln -s /software/biosoftware/netMHCIIpan-4.0/netMHCIIpan /usr/local/bin/

Finish the installation:
a. Copy or link  the 'netMHCIIpan' script  to a directory in the users' path.
b. Copy the 'netMHCIIpan.1' file  to a location  in your manual system.
    If you need a compiled version try running:
    man -d netMHCIIpan.1 |compress >netMHCIIpan.Z
    or:
    neqn netMHCIIpan.1 |tbl |nroff -man |col |compress >netMHCIIpan.Z