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 * -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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