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]
<mailto:[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] <mailto:[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
<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
<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-
<http://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] <mailto:[email protected]>
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