Installation of third party software - CaronLab/MhcVizPipe GitHub Wiki

Installing third-party software

This page provides step-by-step instructions for how to install NetMHCpan, NetMHCIIpan and GibbsCluster.

Downloads

You should have downloaded the following software from DTU Health Tech:

  • NetMHCpan4.1
  • NetMHCIIpan4.0
  • GibbsCluster2.0

If you have not downloaded these yet, go to Downloading third-party software.

Installing/setting up

NetMHCpan

The software comes with a readme file which you need to open and follow the instruction to complete the installation. You need to open the application TextEdit to open the document.

  1. First, uncompress and untar the package
    1. Double click on the netMHCpan-4.1b.linux.tar.gz or netMHCpan-4.1b.darwin.tar.gz in your Downloads folder
      1. On Mac this will produce a directory ‘netMHCpan-4.0’.
      2. In Linux, the archive will open and you will see a folder inside called netMHCpan-4.0. Drag the folder out into your downloads directory.
  2. Then, you need to download another file to complete the installation.
    1. Download the file
      1. Type https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/data.tar.gz in your browser and hit enter
      2. This will start the download. If prompted, choose a location to save it (e.g. Downloads).
      3. Copy this file into the directory NetMHCpan-4.1 from step 1.
      4. Then, untar it as in step 1.
  3. Now you’re good, you have all the required files for NetMHCpan4.1. Now you need to make some changes in the netMHCpan program (or script) to indicate where your files will be stored.
  4. To do this, you need to open the program script with a text editor (e.g. TextEdit).
    1. Go to Downloads/netMHCpan4.1/netMHCpan. Right-click it and choose "Open with" and open it with TextEdit or Text Editor or something similar.
  5. Once the file opened, go under the section GENERAL SETTINGS: CUSTOMIZE TO YOUR SITE. There are 2 lines of code to change to indicate where your files will go:
    1. Under the line # full path to the NetMHCpan 4.0 directory (mandatory), indicate where the directory of netMHCpan-4.0 is located. Here is an example:
    2. setenv NMHOME /Users/isasirois/Downloads/netMHCpan-4.1
      1. You just need to change what is in bold, i.e. your personal location
      2. Save your change (cmd+S or ctrl+s)
    3. Then, under the line # you need to determine where to store temporary files, you will indicate where the files will be stored
    4. You need to make the following change
      1. setenv TMPDIR /scratch into this: setenv TMPDIR $NMHOME/tmp
      2. Save your change (cmd+S or ctrl+s)
    5. Make sure the tmp folder exists, because the programs aren't smart enough to make it for you if it doesn't. So for the above example, you would create a folder called "tmp" inside your NetMHCpan directory. 2. For example, go to ~/Downloads/netMHCpan-4.0 and create a folder there named tmp
  6. You can now close the netMHCpan file. Now you need to copy it in the bin.
    1. Go to Finder and click on Go to. In the black space, type: /usr/local/bin (hit enter). Copy your netMHCpan file that you just modified right there.
Testing NetMHCpan
  1. To be sure that the netMHCPan4.0 is well installed, you need to do a test. This is also indicated in the netMHCpan4.0.readme file under the third section called: ‘ In the ‘netMHCpan-4.0/test’ directory test the software:’
  2. Open your Terminal (Go to Finder/Applications/Utilities/Terminal or via your Launchpad)
    1. You need to indicate to the terminal which directory it should open. Type:
      1. cd /Users/isasirois/Downloads/NetMHCpan-4.1/test and hit enter.
        • Be sure to replace the path with the path to the NetMHCpan-4.0 test folder on YOUR computer.
        • Note there is a space between "cd" and "/"
  3. Then type or copy-paste:
    1. ../netMHCpan -p test.pep > test.pep.myout and hit enter.
    2. ../netMHCpan test.fsa > test.fsa.myout and hit enter.
    3. ../netMHCpan -hlaseq B0702.fsa -p test.pep > test.pep_userMHC.myout and hit enter.
  4. Go into the Test directory via your Finder and open the files with the .out and .myout extensions. At the top of each file will be a lengthy header with all the parameters and settings which were used. Under that there will be a table. For each pair of files (your test file and the one provided as a comparison, e.g. test.fsa.out and test.fsa.myout), the values in the tables should be identical or nearly identical.

Congratulations! NetMHCpan is installed and functional!

NetMHCIIpan

The installation for NetMHCIIpan is quite similar to netMHCpan. There are only few differences like the name of the folders to download and the name of the test files.

  1. First, uncompress and untar the package
    1. Double click on the netMHCIIpan-4.0.linux.tar.gz or netMHCIIpan-4.0.darwin.tar.gz in your Downloads folder
      1. On Mac this will produce a directory ‘netMHCIIpan-4.0’.
      2. In Linux, the archive will open and you will see a folder inside called netMHCIIpan-4.0. Drag the folder out into your downloads directory.
  2. Then, you need to download another file to complete the installation.
    1. Download the file
      1. Type https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/data.tar.gz in your browser and hit enter
      2. This will start the download. If prompted, choose a location to save it (e.g. Downloads).
      3. Copy this file into the directory NetMHCIIpan-4.0 from step 1.
      4. Then, untar it as in step 1.
  3. Now you’re good, you have all the required files for NetMHCIIpan4.0. Now you need to make some changes in the netMHCIIpan program (or script) to indicate where your files will be stored.
  4. To do this, you need to open the program script with a text editor (e.g. TextEdit).
    1. Go to Downloads/netMHCIIpan4.0/netMHCIIpan. Right-click it and choose "Open with" and open it with TextEdit or Text Editor or something similar.
  5. Once the file opened, go under the section GENERAL SETTINGS: CUSTOMIZE TO YOUR SITE. There are 2 lines of code to change to indicate where your files will go:
    1. Under the line # full path to the NetMHCIIpan 4.0 directory (mandatory), indicate where the directory of netMHCpan-4.0 is located. Here is an example:
    2. setenv NMHOME /Users/isasirois/Downloads/netMHCIIpan-4.0
      1. You just need to change what is in bold, i.e. your personal location
      2. Save your change (cmd+S or ctrl+s)
    3. Then, under the line # you need to determine where to store temporary files, you will indicate where the files will be stored
    4. You need to make the following change
      1. setenv TMPDIR /scratch into this: setenv TMPDIR $NMHOME/tmp
      2. Save your change (cmd+S or ctrl+s)
    5. Make sure the tmp folder exists, because the programs aren't smart enough to make it for you if it doesn't. So for the above example, you would create a folder called "tmp" inside your NetMHCIIpan directory. 2. For example, go to ~/Downloads/netMHCpan-4.0 and create a folder there named tmp
  6. You can now close the netMHCIIpan file. Now you need to copy it in the bin.
    1. Go to Finder and click on Go to. In the black space, type: /usr/local/bin (hit enter). Copy your netMHCIIpan file that you just modified right there.
Testing NetMHCIIpan
  1. To be sure that the netMHCIIPan4.0 is well installed, you need to do a test. This is also indicated in the netMHCpan4.0.readme file under the third section called: ‘ In the ‘netMHCIIpan-4.0/test’ directory test the software:’
  2. Open your Terminal (Go to Finder/Applications/Utilities/Terminal or via your Launchpad)
    1. You need to indicate to the terminal which directory it should open. Type:
      1. cd ~/Downloads/NetMHCIIpan-4.0/test and hit enter.
        • Be sure to replace the path with the path to the NetMHCIIpan-4.0 test folder on YOUR computer.
        • Note there is a space between "cd" and "/"
  3. Then type or copy-paste:
    1. ../netMHCIIpan -f example.fsa -a DRB1_0101 > example.fsa.myout and hit enter.
    2. ../netMHCIIpan -f example.pep -inptype 1 -a DRB1_0101 > example.pep.myout and hit enter.
    3. ../netMHCIIpan -f example.fsa -a H-2-IAb -s -u > example.fsa.sorted.myout and hit enter.
    4. ../netMHCIIpan -f example.fsa -hlaseq DRB10101.fsa > example.fsa_hlaseq.myout and hit enter.
    5. ../netMHCIIpan -f example.fsa -hlaseqA alpha.dat -hlaseq beta.dat > example.fsa_hlaseq_A+B.myout and hit enter.
  4. Go into the Test directory via your Finder and open the files with the .out and .myout extensions. At the top of each file will be a lengthy header with all the parameters and settings which were used. Under that there will be a table. For each pair of files (your test file and the one provided as a comparison, e.g. example.fsa.out and example.fsa.myout), the values in the tables should be identical or nearly identical.

Congratulations! NetMHCIIpan is installed and functional!

GibbsCluster

The installation for GibbsCluster is also quite similar to netMHCpan. There are only few differences, such as there are no additional files to download and the names of the test files are different.

  1. First, uncompress and untar the package
    1. Double click on the gibbscluster2.0f.linux.tar.gz or gibbscluster2.0f.darwin.tar.gz in your Downloads folder
      1. On Mac this will produce a directory ‘GibbsCluster-2.0’.
      2. In Linux, the archive will open and you will see a folder inside called GibbsCluster-2.0. Drag the folder out into your downloads directory.
  2. Now you need to make some changes in the GibbsCluster program (or script) to indicate where your files will be stored.
  3. To do this, you need to open the program script with a text editor (e.g. TextEdit).
    1. Go to Downloads/GibbsCluster-2.0/gibbscluster. Right-click it and choose "Open with" and open it with TextEdit or Text Editor or something similar.
  4. Once the file opened, go under the section GENERAL SETTINGS: CUSTOMIZE TO YOUR SITE. There are 2 lines of code to change to indicate where your files will go:
    1. Under the line # Set FULL PATH to the GibbsCluster 2.0 directory (mandatory), indicate where the directory of GibbsCluster-4.0 is located. Here is an example:
    2. setenv GIBBS /Users/isasirois/Downloads/GibbsCluster-2.0
      1. You just need to change what is in bold, i.e. your personal location
      2. Save your change (cmd+S or ctrl+s)
  5. You can now close the gibbscluster file. Now you need to copy it in the bin.
    1. Go to Finder and click on Go to. In the black space, type: /usr/local/bin (hit enter). Copy your gibbscluster file that you just modified right there.
Testing GibbsCluster
  1. To be sure that the GibbsCluster2.0 is well installed, you need to do a test. This is also indicated in the gibbscluster-2.0.readme file under INSTALLATION step 3.
  2. Open your Terminal (Go to Finder/Applications/Utilities/Terminal or via your Launchpad)
    1. You need to indicate to the terminal which directory it should open. Type:
      1. cd ~/Downloads/GibbsCluster-2.0/test and hit enter.
        • Be sure to replace the path with the path to the GibbsCluster-2.0 test folder on YOUR computer.
        • Note there is a space between "cd" and "/"
  3. Then type or copy-paste:
    1. ../gibbscluster -f test.pep -P gibbs > test.pep.myout and hit enter.
    2. ../gibbscluster -f small.pep -P gibbs -C -I 1 -D 5 -g1-4 -S3 > small.pep.myout and hit enter.
  4. Go into the Test directory via your Finder and open the files with the .out and .myout extensions. At the top of each file will be a lengthy header with all the parameters and settings which were used. Under that there will be a table. For each pair of files (your test file and the one provided as a comparison, e.g. test.fsa.out and test.fsa.myout), the values in the tables should be identical or nearly identical.

Congratulations! GibbsCluster is installed and functional!