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 * -- 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.
TPP_error.docx
Description: MS-Word 2007 document