Re: [spctools-discuss] Linux version of TPP
Works great. Thanks a lot Eric. -Kamal On Mon, Nov 19, 2018 at 10:41 AM Eric Deutsch wrote: > 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? > > > > Regards, > > Eric > > > > > > *From:* Kamal Mandal > *Sent:* Monday, November 19, 2018 10:38 AM > *To:* Eric Deutsch > *Cc:* spctools-discuss@googlegroups.com > *Subject:* Re: [spctools-discuss] Linux version of TPP > > > > 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 > 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 > *Sent:* Monday, November 19, 2018 9:27 AM > *To:* Eric Deutsch > *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 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 > 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 > *Sent:* Saturday, November 17, 2018 11:31 PM > *To:* Eric Deutsch > *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 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 > 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 r
RE: [spctools-discuss] Linux version of TPP
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? Regards, Eric *From:* Kamal Mandal *Sent:* Monday, November 19, 2018 10:38 AM *To:* Eric Deutsch *Cc:* spctools-discuss@googlegroups.com *Subject:* Re: [spctools-discuss] Linux version of TPP 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 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 *Sent:* Monday, November 19, 2018 9:27 AM *To:* Eric Deutsch *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 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 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 *Sent:* Saturday, November 17, 2018 11:31 PM *To:* Eric Deutsch *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 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 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 *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'
Re: [spctools-discuss] Linux version of TPP
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 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 > *Sent:* Monday, November 19, 2018 9:27 AM > *To:* Eric Deutsch > *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 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 > 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 > *Sent:* Saturday, November 17, 2018 11:31 PM > *To:* Eric Deutsch > *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 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 > 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 thi
RE: [spctools-discuss] Linux version of TPP
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 *Sent:* Monday, November 19, 2018 9:27 AM *To:* Eric Deutsch *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 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 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 *Sent:* Saturday, November 17, 2018 11:31 PM *To:* Eric Deutsch *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 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 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 *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 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
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 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 > 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 >> *Sent:* Saturday, November 17, 2018 11:31 PM >> *To:* Eric Deutsch >> *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 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 >> *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
RE: [spctools-discuss] Linux version of TPP
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 *Sent:* Saturday, November 17, 2018 11:31 PM *To:* Eric Deutsch *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 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 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 *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 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 *On Behalf Of *Kamal Mandal *Sent:* Thursday, November 15, 2018 7:02 PM *To:* spctools-discuss *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
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 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 > 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 >> *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 >> 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 ma
Re: [spctools-discuss] Linux version of TPP
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 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 > *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 > 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 > *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. >
RE: [spctools-discuss] Linux version of TPP
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 *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 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 *On Behalf Of *Kamal Mandal *Sent:* Thursday, November 15, 2018 7:02 PM *To:* spctools-discuss *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 * -- 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.co
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 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 > *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 * -- 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.
RE: [spctools-discuss] Linux version of TPP
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 *On Behalf Of *Kamal Mandal *Sent:* Thursday, November 15, 2018 7:02 PM *To:* spctools-discuss *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 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.
