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 < [email protected]> 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 <[email protected]> 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, >> [email protected] 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 >>> [email protected] >>> >>> -- >> 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 [email protected]. >> To post to this group, send email to [email protected]. >> 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 > [email protected] > > -- > 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 > [email protected]. > To post to this group, send email to [email protected]. > 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 [email protected]. > To post to this group, send email to [email protected]. > 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 [email protected] -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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