[Xi Wang]

Last time I successfully installed Cufflinks using the option --with-boost=/PATH/TO/BOOST/ROOT when configuring. I give my solution here.

1. get the path to boost root, in which there are at least two dirs: include and lib
2. cd into the dir cufflinks-0.8.1
* type ./configure --with-boost=/PATH/TO/BOOST/ROOT
* type make
* type make install

Let me know if this trial fails.

[BioTalk]

Yes I downloaded boost library and try to add path to it with the command path=<home/path to the boost folder...>.

I do not know if there is anything else I need to do!

Thank you

[BioTalk]

Last time I successfully installed Cufflinks using the option --with-boost=/PATH/TO/BOOST/ROOT when configuring. I give my solution here.

1. get the path to boost root, in which there are at least two dirs: include and lib
2. cd into the dir cufflinks-0.8.1
* type ./configure --with-boost=/PATH/TO/BOOST/ROOT
* type make
* type make install

Let me know if this trial fails.

Thank you for your prompt reply.

I did not understand how 1st step works? i.e How to get a path to boost root. Also I searched boost folder, I found Lib Directory but can not see include directory in it. PLease let me know how this works.

Thank you.

[BioTalk]

Thank you everyone for the help.

[Xi Wang]

Thank you everyone for the help.

Have you solved this problem? I didn't hear from you any more:-)

[Utrecht]

I seem to be having the same problem. I am trying to install Cufflinks on a 32 bit Linux system, for which there are no pre-compiled binaries available (only 64 bit). I successfully built the Boost package using bjam, as instructed on the Getting Started page of Cufflinks.
Then I ran ./configure in the cufflinks directory, which gave no obvious errors (the Boost package was found, too). However, when I run 'make' there are several error messages that I don't understand (see below). Specially the '-m64' argument is suspicious, does this mean that it is trying to compile in 64 bit mode? I don't have enough experience with Linux to know how to proceed.
How did other people do this? Or is everyone using a 64 bit system? I have none available, as far as I know.
Any help would be greatly appreciated! Thanks..

Output after running 'make':

rob@robin:~/cufflinks-0.8.2$ make
make  all-recursive
make[1]: Entering directory `/home/robin/cufflinks-0.8.2'
Making all in src
make[2]: Entering directory `/home/robin/cufflinks-0.8.2/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src    -Wall -Wno-strict-aliasing -g -gdwarf-2 -m64 -O3  -DNDEBUG  -pthread -I/usr/local/include -MT clustering.o -MD -MP -MF ".deps/clustering.Tpo" -c -o clustering.o clustering.cpp; \
	then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po"; else rm -f ".deps/clustering.Tpo"; exit 1; fi
In file included from /usr/include/features.h:354,
                 from /usr/include/assert.h:37,
                 from /usr/include/c++/4.2/cassert:49,
                 from /usr/local/include/boost/graph/vector_as_graph.hpp:17,
                 from clustering.h:17,
                 from clustering.cpp:10:
/usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such file or directory
In file included from clustering.cpp:10:
clustering.h:29:41: error: boost/vector_property_map.hpp: No such file or directory
clustering.h:142:7: warning: no newline at end of file
make[2]: *** [clustering.o] Error 1
make[2]: Leaving directory `/home/robin/cufflinks-0.8.2/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/robin/cufflinks-0.8.2'
make: *** [all] Error 2

[BioTalk]

I too experienced the same kind of problem with Cufflinks in 32 bit system. It was a problem because of 32 bit OS, as the binary available for 32 bit is getting compiled into 64bit and therefore it is of no use. I would suggest you to install cufflinks in 64 bit machine.

Thanks!

[Utrecht]

Thanks BioTalk, unfortunately I don't have a 64 bit system available right now, so I'll have to think of something else...

[repinementer]

finding boost package in cufflinks

Hi all

The discussion is ended abruptly with out any answer
I was installed boost and bjam and built them on usr\local and after that ran ./configure but it is not detecting boost libraries.
i have added boost libraries to path also.

Then I ran ./configure in the cufflinks directory, which gave errors (the Boost package was not found).

PS:I'm using 32 bit computer and downloaded 32 bit boost packages

[bogugk@Trivia ~]$ [B]cd /usr/local/boost_1_41_0/[/B]
[bogugk@Trivia boost_1_41_0]$ [B]ls -l[/B]
total 320
drwxr-xr-x  3 root   root   4096 Jan  8 15:18 bin.v2
-rwxr-xr-x  1 root   root 171424 Jan  8 15:17 bjam
drwxr-xr-x 74    400  401  12288 Nov 18  2009 boost
-rw-r--r--  1    400  401    849 Nov 13  2009 boost-build.jam
-rw-r--r--  1    400  401    989 Nov 13  2009 boost.css
-rw-r--r--  1    400  401   6308 Nov 13  2009 boost.png
-rw-r--r--  1    400  401   1958 Nov 13  2009 bootstrap.bat
-rw-r--r--  1 root   root    852 Jan  8 15:17 bootstrap.log
-rwxr-xr-x  1    400  401  10211 Nov 13  2009 bootstrap.sh
-rw-r--r--  1    400  401    427 Nov 13  2009 CMakeLists.txt
drwxr-xr-x  7    400  401   4096 Nov 18  2009 doc
-rw-r--r--  1    400  401    770 Nov 13  2009 index.htm
-rw-r--r--  1    400  401   5485 Nov 13  2009 index.html
-rw-r--r--  1    400  401    291 Nov 13  2009 INSTALL
-rw-r--r--  1    400  401  23355 Nov 13  2009 Jamroot
drwxr-xr-x 85    400  401   4096 Nov 18  2009 libs
-rw-r--r--  1    400  401   1338 Nov 13  2009 LICENSE_1_0.txt
drwxr-xr-x  4    400  401   4096 Nov 18  2009 more
drwxr-xr-x  2    400  401   4096 Nov 18  2009 people
-rw-r--r--  1 root   root    822 Jan  8 15:17 project-config.jam
-rwxrwxrwx  1 gisv12  401   6009 Nov 18  2009 README.txt
-rw-r--r--  1    400  401   2610 Nov 13  2009 rst.css
drwxr-xr-x  3 root   root   4096 Jan  8 15:18 stage
drwxr-xr-x  2    400  401   4096 Nov 18  2009 status
drwxr-xr-x 13    400  401   4096 Nov 18  2009 tools
drwxr-xr-x  2    400  401   4096 Nov 18  2009 wiki

[B]./configure --with-boost=/usr/local/boost_1_41_0/boost/[/B]
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) gawk
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking for boostlib >= 1.38.0... configure: error: We could not detect the boost libraries (version 1.38 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option.  If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.

[Utrecht]

Did you use bjam to build Boost? You can find instructions here: http://cufflinks.cbcb.umd.edu/tutorial.html

But anyway, this didn't work for me in the end. It would seem that cufflinks doesn't compile properly on a 32 bit system, so I used a MacBook (to run a few tests) and a 64 bit system (to do the actual analysis) instead.

[repinementer]

yes 32 bit is not working

yes i used bjam.
yes i agree some thing wrong with 32 bit
seems 64 bit doesnt have any configure file so no need to run the commands??????????

./configure --prefix=/path/to/cufflinks/install --with-boost=/path/to/boost
make
make install

but ./command (ex: ./cufflinks) are working fine

[bogugk@Trivia cufflinks-0.8.2.Linux_x86_64]$ ./cufflinks ./test_data.sam
Counting hits in map
Total map density: 104.000000
Processing bundle [ test_chromosome:52-550 ] with 99 non-redundant alignments

[Utrecht]

That's right, there are pre-compiled binaries for 64 bit systems and/or Macs. Much easier, eh? :-)

[repinementer]

FluxCapacitor and FluxStimulator

Have you installed these?
Seems pretty google code RNASEQ tools.

http://flux.sammeth.net/cap_installation.html

[emucaki]

Gonna bump this thread again. I was able to get through all the boost and sam/bam issues for this installation (I've successfully installed bowtie and tophat as well), but now with Cufflinks I'm having a 'make' error (it is a 64 bit system).

GList.hh(413): remark #981: operands are evaluated in unspecified order
if (Found(item, result)) return true;
^

compilation aborted for clustering.cpp (code 2)
make[2]: *** [clustering.o] Error 1
make[2]: Leaving directory `/work/emucaki/goblin/Cufflinks/cufflinks-0.9.1/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/work/emucaki/goblin/Cufflinks/cufflinks-0.9.1'
make: *** [all] Error 2

Any ideas?

[jmarshall]

GList.hh(413): remark #981: operands are evaluated in unspecified order

You are using Intel's compiler and you have configured cufflinks so as to compile with -Werror.

This is a relatively useless warning, and it's hard to see why it's being triggered by this code. It seems that the usual advice is to switch the warning off: http://software.intel.com/en-us/foru...ad.php?t=62309.