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
>>
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>>
>>
>> --
>>
>> 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 *

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