Mohammad, For the most part the tutorial should work on either platform. You'll have to change the paths obviously as they'll be different. Just shout out to the mailing list if you run into problems and you're sure to get help.
-Joe On Sun, May 31, 2015 at 5:35 AM, Mohammad T Islam < md.is...@students.mq.edu.au> wrote: > Hi Joe, > > Thanks a lot! After installing *patch* I was able to complete the TPP > installation. I haven't used TPP before so I will go through the tutorial > soon. On a side note, I noticed the tutorials are windows based. Are there > any linux specific user guide? > > Thank you > > Best Regards > Mohammad > > > > > On 30/05/2015 3:00 pm, Joseph Slagel wrote: > > I'm sorry, I should have read more closely. The line: > > /bin/sh: 4: patch: not found > > seems to suggest that you don't have the "patch" program on your system. > Try running > > sudo apt-get update && sudo apt-get install patch > > > to update your system and install the patch program. > > > On Fri, May 29, 2015 at 5:39 PM, Mohammad T Islam < > md.is...@students.mq.edu.au> wrote: > >> Hi Joe, >> >> Thanks for your reply. hdf5-1.8.6.gcc47patch is available in the *extern* >> folder. >> >> *Ubuntu 14.04* >> ubuntu@trans-proteomic-pipeline-server:~$ ls -al >> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/*patch >> -rwxrwxr-x 1 51842 1100 1820 Nov 7 2013 >> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/boost_1_54_0.mingwpatch >> -rw-rw-r-- 1 51842 1100 967 May 30 2014 >> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/boost_1_54_0.ubuntupatch >> -rw-rw-r-- 1 51842 1100 944 Dec 28 2012 >> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch >> -rw-rw-r-- 1 51842 1100 7042 Sep 5 2012 >> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.mingwpatch >> >> *Ubuntu 12.04* >> ubuntu@trans-proteomic-pipeline:~$ ls -al >> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/*patch >> -rwxrwxr-x 1 51842 1100 1820 Nov 7 2013 >> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/boost_1_54_0.mingwpatch >> -rw-rw-r-- 1 51842 1100 967 May 29 2014 >> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/boost_1_54_0.ubuntupatch >> -rw-rw-r-- 1 51842 1100 944 Dec 28 2012 >> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch >> -rw-rw-r-- 1 51842 1100 7042 Sep 5 2012 >> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.mingwpatch >> >> I followed the sourceforge site link from the wiki >> <http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP#Source_Code_Installation_.28For_Linux_systems.29> >> and downloaded the TPP_4.8.0-src.tgz file. >> >> Direct link for this file was >> >> >> http://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.8%20%28philae%29%20rev%200/TPP_4.8.0-src.tgz?r=http%3A%2F%2Ftools.proteomecenter.org%2Fwiki%2Findex.php%3Ftitle%3DSoftware%3ATPP&ts=1432642452&use_mirror=softlayer-sng >> >> >> Best Regards >> Mohammad >> >> >> >> On 30/05/2015 2:39 am, Joseph Slagel wrote: >> >> It appears as if you are missing the following file: >> >> >> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch >> >> Can you look to see what *patch files you have in this directory? And >> did you download the source tar archive or did you check out the code from >> the sourceforge svn repository? >> >> -Joe >> >> >> On Thu, May 28, 2015 at 10:38 AM, MD <md.is...@students.mq.edu.au> wrote: >> >>> Hi Joe, >>> >>> I am trying to install 4.8 on linux and getting the following error. I >>> also tried 4.71 , and both on ubuntu 12.04 and 14.04. . Can you please >>> help? >>> >>> tu-x86_64 ZLIB_INCL="" ZLIB_LIB=-lz STATIC_LIBSTDCPP= >>> >>> make[1]: Entering directory >>> `/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/extern/gzstream' >>> >>> g++ -I. -O -c -o Ubuntu-x86_64gzstream.o gzstream.cpp >>> >>> ar cr >>> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/libgzstream.a >>> Ubuntu-x86_64gzstream.o >>> >>> make[1]: Leaving directory >>> `/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/extern/gzstream' >>> >>> uncompressing HDF5 library >>> >>> mkdir -p >>> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/hdf5-1.8.6 >>> >>> cd >>> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/hdf5-1.8.6; >>> cd ..; tar zxf >>> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.tar.gz; >>> \ >>> >>> for P in >>> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch >>> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.mingwpatch; >>> do \ >>> >>> echo "applying HDF5 patch $P"; \ >>> >>> patch -s -p0 < $P; \ >>> >>> done >>> >>> applying HDF5 patch >>> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch >>> >>> /bin/sh: 4: patch: not found >>> >>> applying HDF5 patch >>> /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.mingwpatch >>> >>> /bin/sh: 4: patch: not found >>> >>> make: *** >>> [/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/hdf5-1.8.6] >>> Error 127 >>> >>> >>> root@trans-proteomic-pipeline:/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src# >>> >>> >>> >>> >>> Thank you >>> >>> Regards >>> Mohammad >>> >>> On Saturday, November 22, 2014 at 9:07:05 AM UTC+11, >>> jsl...@systemsbiology.org wrote: >>>> >>>> Announcing the official release of Trans-Proteomic Pipeline (TPP) 4.8.0 >>>> "PHILAE" >>>> >>>> We are proud to offer a update to the Trans-Proteomic Pipeline (TPP) >>>> software, release 4.8.0 (4.8 revision). The software is available for >>>> Windows as well as Linux (and unofficially) through OSX source from all the >>>> usual locations (please see the section below, "Getting the software"). >>>> Most users are recommended to use the Windows installer, which installs and >>>> configures the TPP and other required software (such as a web >>>> server). For advanced users who need to customize the TPP, or for >>>> those who run on Linux or OS X, you can download the source code. >>>> >>>> >>>> == Release Notes == >>>> >>>> * Release notes on the most important new features, changes, and known >>>> issues are available at: >>>> >>>> "http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.8 >>>> .0_Release_Notes" >>>> >>>> >>>> == Getting the TPP Software == >>>> >>>> * Download the TPP version 4.8.0 native windows installer from the >>>> Sashimi SourceForge project file release page: >>>> >>>> "http://sourceforge.net/ >>>> <http://goog_2056063534>http://sourceforge.net/projects/sashimi/files/Trans-Proteomic >>>> Pipeline (TPP) >>>> <http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29> >>>> " >>>> >>>> * Everyone is encouraged to read and contribute to our wiki, at >>>> "http://tools.proteomecenter.org/wiki/"; >>>> >>>> * For guides to installing and using our software, please see our wiki: >>>> "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP"; >>>> >>>> * For downloading the source code, please go to the following link: >>>> "http://sourceforge.net/projects/sashimi/files/"; and find the 4.8.0 >>>> source code .zip package; >>>> or, check out the code directly from svn: >>>> "svn co svn://svn.code.sf.net/p/sashimi/code/tags/release_4-8-0" >>>> >>>> For building from source, please refer to the README and INSTALL files >>>> in src/ directory of TPP as well as the wiki. >>>> >>>> >>>> == Acknowledgements == >>>> >>>> The TPP Team: Luis, David, Mike, and Joe, plus all other developers >>>> who contributed to this release from the ISB. Thanks to developers >>>> and users from the TPP's user community who also provide feedback and >>>> code contributions. >>>> >>>> >>>> -- >>>> Joe Slagel >>>> Institute for Systems Biology >>>> jsla...@systemsbiology.org >>>> >>>> -- >>> 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 http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> >> >> -- >> Joe Slagel >> Institute for Systems Biology >> jsla...@systemsbiology.org >> >> -- >> 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/GHrtZqh_aQI/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 http://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 http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > > > -- > Joe Slagel > Institute for Systems Biology > jsla...@systemsbiology.org > > -- > 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/GHrtZqh_aQI/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 http://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 http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- Joe Slagel Institute for Systems Biology jsla...@systemsbiology.org -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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