Looks like its working. But I have to either add all the executable files as global aliases or I have to use complete address all the time. Anyway, its better than not having tpp at all. Can you suggest any better to handle it?
-Kamal On Mon, Nov 19, 2018 at 9:45 AM Eric Deutsch <edeut...@systemsbiology.org> wrote: > 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. > > > > Regards, > > Eric > > > > > > > > *From:* Kamal Mandal <kamal...@gmail.com> > *Sent:* Monday, November 19, 2018 9:27 AM > *To:* Eric Deutsch <edeut...@systemsbiology.org> > *Cc:* spctools-discuss@googlegroups.com > *Subject:* Re: [spctools-discuss] Linux version of TPP > > > > Hi Eric, > > I heard the following reply from our system administrator. Can you please > go through it and suggest me some alternative. > > > > "I would recommend not installing the static versions of libstdc++ and > glibc and fixing the "Trans-Proteomics Pipeline" to use the shared > versions. If only because the shared versions are maintained by us, the > wynton administrators. If the pipeline is statically linked, then it > should be recompiled/relinked everytime the system is updated. There can > be a speed advantage with static linking, but without a benchmark showing a > big advantage, it's not worth the maintenance headache." > > > > -Kamal > > > > On Sun, Nov 18, 2018 at 10:50 PM Kamal Mandal <kamal...@gmail.com> wrote: > > Thanks a lot Eric. I will check that with the administrator and let you > know. > > > > -Kamal > > > > On Sun, Nov 18, 2018 at 10:46 PM Eric Deutsch <edeut...@systemsbiology.org> > wrote: > > 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, > > Eric > > > > > > > > *From:* Kamal Mandal <kamal...@gmail.com> > *Sent:* Saturday, November 17, 2018 11:31 PM > *To:* Eric Deutsch <edeut...@systemsbiology.org> > *Cc:* spctools-discuss@googlegroups.com > *Subject:* Re: [spctools-discuss] Linux version of TPP > > > > Hi Eric, > > I managed to get svn. Though I had to use "http://svn.code.sf.net > <http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline>" > instead of "svn://svn.code.sf.net > <http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline>". > I don't know if that makes any difference. > > However, I am getting an error while compiling - "make all". > > Please find the attached file containing the error message. > > Please suggest the needful. > > > > -Kamal > > > > On Thu, Nov 15, 2018 at 11:28 PM Kamal Mandal <kamal...@gmail.com> wrote: > > Eric, > > I would like to get the tarball of TPP. That might help. I can ask our > administrator to install these dependencies. > > Regarding docker- I tried "docker --version", it said "command not found". > > > > Thanks, > > > > -Kamal > > > > On Thu, Nov 15, 2018 at 11:19 PM Eric Deutsch <edeut...@systemsbiology.org> > wrote: > > 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 > > > > > > > > > > > > *From:* Kamal Mandal <kamal...@gmail.com> > *Sent:* Thursday, November 15, 2018 9:44 PM > *To:* spctools-discuss@googlegroups.com > *Cc:* edeut...@systemsbiology.org > *Subject:* Re: [spctools-discuss] Linux version of TPP > > > > HI Eric, > > Thanks a lot for your quick response. Actually I tried this way but didn't > work. I am not very much expert in computation, but it looks like "svn" > command is not working in our cluster. I thought if I download the entire > package, that might help. > > Can you suggest some way out of it? Here is the specification of our > cluster - "CentOS Linux 7 (Core)" > > > > -Kamal > > > > On Thu, Nov 15, 2018 at 9:07 PM Eric Deutsch <edeut...@systemsbiology.org> > wrote: > > 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 > > > > > > *From:* spctools-discuss@googlegroups.com < > spctools-discuss@googlegroups.com> *On Behalf Of *Kamal Mandal > *Sent:* Thursday, November 15, 2018 7:02 PM > *To:* spctools-discuss <spctools-discuss@googlegroups.com> > *Subject:* [spctools-discuss] Linux version of TPP > > > > Hello, > > Can anybody help me with the link for downloading the linux version of > TPP. > > The available recipe of installation doesn't work for me since I cannot > use "sudo" in our cluster. I can install it only in my own space. > > > > -Kamal > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/GOYhdTTMOJo/unsubscribe > . > To unsubscribe from this group and all its topics, send an email to > spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > > > > > -- > > Kamal Mandal, M.Tech > > Research Scholar > > National Institute of Immunology, New Delhi > > Aruna Asaf Ali Marg > > New Delhi - 110067 > > *India* > > > > *Contact no. :- +91- 9560445356 * > > > > > -- > > Kamal Mandal, M.Tech > > Research Scholar > > National Institute of Immunology, New Delhi > > Aruna Asaf Ali Marg > > New Delhi - 110067 > > *India* > > > > *Contact no. :- +91- 9560445356 * > > > > > -- > > Kamal Mandal, M.Tech > > Research Scholar > > National Institute of Immunology, New Delhi > > Aruna Asaf Ali Marg > > New Delhi - 110067 > > *India* > > > > *Contact no. :- +91- 9560445356 * > > > > > -- > > Kamal Mandal, M.Tech > > Research Scholar > > National Institute of Immunology, New Delhi > > Aruna Asaf Ali Marg > > New Delhi - 110067 > > *India* > > > > *Contact no. :- +91- 9560445356 * > > > > > -- > > Kamal Mandal, M.Tech > > Research Scholar > > National Institute of Immunology, New Delhi > > Aruna Asaf Ali Marg > > New Delhi - 110067 > > *India* > > > > *Contact no. :- +91- 9560445356 * > -- Kamal Mandal, M.Tech Research Scholar National Institute of Immunology, New Delhi Aruna Asaf Ali Marg New Delhi - 110067 *India* *Contact no. :- +91- 9560445356 * -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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