Linux version of TPP
Kamal Mandal
Eric Deutsch
Hi Kamal, I’m not certain what would be best, but suppose you just install the TPP in your own area under your username. So, based on the instructions here:
http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS
You could install TPP in a space off your home directory and then use it that way on the cluster. Maybe something like this:
Assume your home directory is /home/kmandal, you could try something like this:
cd /home/kmandal
mkdir tpp svn data
cd svn
svn checkout svn://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline
echo "INSTALL_DIR = /users/kmandal/tpp" > site.mk
echo "TPP_DATADIR = /users/kmandal/data" >> site.mk
make all
make install
If that all works, then the TPP executables are all in /users/kmandal/tpp/bin
The possible snag is that you still need to have the equivalents of these requirements installed on your machine to compile it:
sudo apt --yes install subversion
sudo apt --yes install build-essential
sudo apt --yes install perl
sudo apt --yes install zlib1g-dev
sudo apt --yes install libghc-bzlib-dev
sudo apt --yes install gnuplot
sudo apt --yes install unzip
sudo apt --yes install expat
sudo apt --yes install libexpat1-dev
Maybe your machine has all these already, or maybe not. Do you have a sys administrator that you can ask to install those components?
What version of Linux is your cluster running, do you know?
Regards,
Eric
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Eric Deutsch
Hi Kamal, I can post a tarball of the latest code if you’d like to download that and try compiling it. However, there are a substantial number of other requirements. I just launched a fresh CentOS 7.5 node and tried to compile TPP. I found the following dependencies needed to be installed before it would work nicely:
sudo yum -y install subversion
sudo yum -y groupinstall 'Development Tools'
sudo yum -y install gnuplot
sudo yum -y install gd-devel
sudo yum -y install libzip-devel
sudo yum -y install bzip2-devel
sudo yum -y install libstdc++-static
sudo yum -y install glibc-static
sudo yum -y install perl-devel
If you have someone you can ask to install those, then you should be able to build TPP. If you cannot ask anyone to install such things for you, then this may be difficult.
Is there Docker available on your machine/cluster? That would make it easier.
Regards,
Eric
Kamal Mandal
Kamal Mandal
Eric Deutsch
Hi Kamal, glad you got subversion working. Odd that svn:// did not work but http did, but that’s fine, they are equivalent for this purpose.
The error messages in your attachment look like what you would get this these yums were not run:
sudo yum -y install libstdc++-static
sudo yum -y install glibc-static
You probably need all of the packages I listed in the previous message downthread. Can you check to see if those were installed?
Thanks,
Kamal Mandal
Thanks a lot Eric. I will check that with the administrator and let you know.-Kamal
Eric Deutsch
Hi Kamal, you could try downloading and trying to run these binaries compiled under CentOS 7.5:
cd ~
wget http://www.tppms.org/sw/TPP5.2RC4/tppUsrLocalTpp-CentOS7.5.tgz
tar -zxf tppUsrLocalTpp-CentOS7.5.tgz
(this will create a tpp/ directory with the TPP programs in it. Test it with the following)
tpp/bin/comet -p
tpp/bin/xinteract
See if that works for you. The `comet` command will run and create a comet.params.new file in the current working directory. The xinteract will generate a usage statement.
Kamal Mandal
Eric Deutsch
If I understand your question correctly, just add the TPP bin directory to your PATH, so with bash:
export PATH=$HOME/tpp/bin:$PATH
now you can just do:
xinteract
Is that what you mean?