Help installing Cufflinks 2.0.1 on Cygwin

[BenS]

Hi all,

I'm trying to install Cufflinks on my windows 7 computer using cygwin, I've searched through the forums, but there doesn't seem to be a solution to this specific problem. The version of Boost I have installed is 1.50. I believe the problem lies somehow with the 'sqrtl' function that it mentions toward the end. I am pretty new to cygwin, so please forgive me if I might have any terminology questions.

I'm posting below the results from me running the ./configure and make commands.


BenS @BenS-HP /cygdrive/c/analysistools/cufflinks-2.0.1
$ ./configure --prefix=/cygdrive/c/analysistools/cufflinks --with-boost=/cygdrive/c/AnalysisTools/boost --with-bam=/cygdrive/c/analysistools/
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) gawk
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
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 Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.6
checking for python platform... cygwin
checking for python script directory... ${prefix}/lib/python2.6/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.6/site-packages
checking for boostlib >= 1.47.0... yes
checking for bamlib... yes
checking build system type... i686-pc-cygwin
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... (cached) yes
checking zlib in /usr... ok
checking for eigenlib... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking for ptrdiff_t... yes
checking host system type... i686-pc-cygwin
checking if gcc accepts -m64... no
checking for struct sysinfo.totalram... yes
checking whether sysctl is declared... no
checking whether CTL_HW is declared... no
checking whether HW_PHYSMEM is declared... no
checking how to create a pax tar archive... gnutar
checking dependency style of gcc... (cached) gcc3
checking dependency style of g++... (cached) gcc3
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands

-- cufflinks 2.0.1 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/c/analysistools/samtools/samtools/include -I/usr/local/include
GCC version: gcc (GCC) 4.5.3
Host System type: i686-pc-cygwin
Install prefix: /cygdrive/c/analysistools/cufflinks
Install eprefix: ${prefix}

See config.h for further configuration information.
Email <[email protected]> with questions and bug reports.


Here are the make results:


BenS@BenS-HP /cygdrive/c/analysistools/cufflinks-2.0.1
$ make
make all-recursive
make[1]: Entering directory `/cygdrive/c/analysistools/cufflinks-2.0.1'
Making all in src
make[2]: Entering directory `/cygdrive/c/analysistools/cufflinks-2.0.1/src'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITSools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT clustering.o -MD -MP -MF .deps/clustering.T
g++: unrecognized option '-pthread'
mv -f .deps/clustering.Tpo .deps/clustering.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITSools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT differential.o -MD -MP -MF .deps/differenti
g++: unrecognized option '-pthread'
In file included from differential.h:29:0,
from differential.cpp:18:
replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’:
replicates.h:152:50: warning: unused variable ‘s2’
In file included from differential.cpp:18:0:
differential.h: In constructor ‘FPKMContext::FPKMContext(double, double, double, double, const CountPerReplicateTable&, double, const FPKMPertusPerReplicateTable&)’:
differential.h:142:21: warning: ‘FPKMContext::status’ will be initialized after
differential.h:139:29: warning: ‘StatusPerReplicateTable FPKMContext::status_per_rep’
differential.h:131:2: warning: when initialized here
differential.cpp: In member function ‘void TestLauncher:erform_testing(std::vector<boost::shared_ptr<SampleAbundances> >&)’:
differential.cpp:212:31: warning: unused variable ‘s2’
differential.cpp: In member function ‘void TestLauncher::record_tracking_data(std::vector<boost::shared_ptr<SampleAbundances> >&)’:
differential.cpp:240:31: warning: unused variable ‘s2’
differential.cpp: In function ‘SampleDifference get_ds_tests(const AbundanceGroup&, const AbundanceGroup&, bool)’:
differential.cpp:790:16: warning: unused variable ‘name’
differential.cpp: In function ‘void test_differential(const std::string&, const std::vector<boost::shared_ptr<SampleAbundances> >&, Tests&, T
differential.cpp:1771:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1772:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1814:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1815:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1856:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1857:83: warning: comparison between signed and unsigned integer expressions
mv -f .deps/differential.Tpo .deps/differential.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITSools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT common.o -MD -MP -MF .deps/common.Tpo -c -o
g++: unrecognized option '-pthread'
In file included from common.cpp:28:0:
replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’:
replicates.h:152:50: warning: unused variable ‘s2’
mv -f .deps/common.Tpo .deps/common.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITSools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT assemble.o -MD -MP -MF .deps/assemble.Tpo -
g++: unrecognized option '-pthread'
mv -f .deps/assemble.Tpo .deps/assemble.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITSools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT tokenize.o -MD -MP -MF .deps/tokenize.Tpo -
g++: unrecognized option '-pthread'
mv -f .deps/tokenize.Tpo .deps/tokenize.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITSools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT abundances.o -MD -MP -MF .deps/abundances.T
g++: unrecognized option '-pthread'
In file included from abundances.cpp:35:0:
replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’:
replicates.h:152:50: warning: unused variable ‘s2’
abundances.cpp: In function ‘void collapse_equivalent_hits(const std::vector<MateHit>&, std::vector<boost::shared_ptr<Abundance> >&, std::vecteHit>&, std::vector<double>&, bool)’:
abundances.cpp:769:28: warning: comparison between signed and unsigned integer expressions
abundances.cpp: In function ‘long double solve_beta(long double, long double, long double)’:
abundances.cpp:1227:145: error: ‘sqrtl’ was not declared in this scope
abundances.cpp: In member function ‘void AbundanceGroup::calculate_FPKM_covariance()’:
abundances.cpp:1780:24: warning: unused variable ‘fpkm’
abundances.cpp: In function ‘void calculate_assignment_probs(const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::VectorXd&, Eigen::M
abundances.cpp:2205:58: warning: comparison between signed and unsigned integer expressions
abundances.cpp: In function ‘AbundanceStatus gamma_mle(const std::vector<boost::shared_ptr<Abundance> >&, const std::vector<MateHit>&, const
abundances.cpp:3300:48: warning: comparison between signed and unsigned integer expressions
abundances.cpp:3302:52: warning: comparison between signed and unsigned integer expressions
In file included from abundances.cpp:36:0:
sampling.h: In function ‘double boost::numeric::ublas::cholesky_factorize(M&) [with M = boost::numeric::ublas::matrix<double>]’:
abundances.cpp:117:45: instantiated from here
sampling.h:83:7: error: ‘sqrtl’ was not declared in this scope
/cygdrive/c/AnalysisTools/boost/include/boost/system/error_code.hpp: At global scope:
/cygdrive/c/AnalysisTools/boost/include/boost/system/error_code.hpp:214:36: warning: ‘boost::system:osix_category’ defined but not used
/cygdrive/c/AnalysisTools/boost/include/boost/system/error_code.hpp:215:36: warning: ‘boost::system::errno_ecat’ defined but not used
/cygdrive/c/AnalysisTools/boost/include/boost/system/error_code.hpp:216:36: warning: ‘boost::system::native_ecat’ defined but not used
Makefile:1444: recipe for target `abundances.o' failed
make[2]: *** [abundances.o] Error 1
make[2]: Leaving directory `/cygdrive/c/analysistools/cufflinks-2.0.1/src'
Makefile:290: recipe for target `all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/cygdrive/c/analysistools/cufflinks-2.0.1'
Makefile:228: recipe for target `all' failed
make: *** [all] Error 2



If anyone has an idea of how to help me, please post, I have tried a great deal of different options, and would like to avoid having to install a separate operating system on my computer to run true Unix if possible. I would be grateful for any help that would fix this situation.

[IBseq]

Hi Ben,
did u manage to install cufflinks?
I am not very good in bioinformatics and I 'm also trying to get cufflinks on windows since I don't have access to a unix machine. All i wanted was to use cummeRbund...

let me know if you made any progress!

Irene

[BenS]

No, I have yet to figure that out, I actually just ended up using galaxy for the work anyway. I do want to be able to use CummeRbund eventually, but no solutions have come yet.

[IBseq]

Hi Ben,
is there any reason why you are not using UNIX/LINUX?
My prob is that i do not have access to it,so I wanted to install on windows...

I will let you know eventually,
Best
irene

[BenS]

My reasoning pretty much the same: I do not have access to UNIX/LINUX currently. This is why I'm attempting to use Cygwin (a UNIX emulator).

There is the possibility to partition my hard drive to attempt to install cufflinks through installing a Linux partition, but I would prefer to avoid that if at all possible, since that would require cutting off large portions of my hard drive dedicated to the storage in the partition, and the exchange between partitions.

So yeah, I would like to be able to use cufflinks and all of its extensions fully, but I've been running into error after error in the process which has pretty much had me run to galaxy to do my analysis (although it doesn't let me use a lot of the possible extra programs that I need cufflinks installed to run properly.)

My best advice would be to keep trying, I've been able to get several things to work thus far by using a combination of Cygwin and the Command Prompt, it's just cufflinks that is giving me a problem, and I'm not even sure if that's necessarily because of the operating system, as many UNIX only programs work just fine with cygwin.

- Ben

[IBseq]

cygwin

Hi Ben,
I have cygwin on my pc now.

It might sound a bit silly question, but I have no idea what to do now:
when i open it, as expected I have the interface where i have to type the commands.

My questions:
how do i import my data into it?and how can i install programs and use them to analyse my data, such as cummerbund?

hope you can help out!
best
irene

[BenS]

Hi Ben,
I have cygwin on my pc now.

It might sound a bit silly question, but I have no idea what to do now:
when i open it, as expected I have the interface where i have to type the commands.

My questions:
how do i import my data into it?and how can i install programs and use them to analyse my data, such as cummerbund?

hope you can help out!
best
irene

Irene,
Cygwin does not require importing into it, since all Cygwin does is emulate a UNIX environment on your computer, all you need to do is navigate to the files on your computer using Cygwin and run them using UNIX style commands.
Note: CummeRbund will require you to have both R and cufflinks on the computer.

When your installing packages during the setup for Cygwin (Note: all you need to do to install more packages in Cygwin is to run Setup.exe again, no reinstallation or uninstallation involved) you will want to check off the packages for R, C++ compiler, the makefile commands, and a few others to make sure you can install.

I've tended to install more than I need just to be safe.

Once you have R (ver 2.7 or above) and cufflinks (I believe the current cummeRbund work with 2.0 or above, but it could be 1.1.0), theoretically all you should need to do is go into R and type:
If you've downloaded them:
install.packages("cummeRbund", dependencies = TRUE)

From Bioconductor:
source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")

[IBseq]

Hi Ben, thanks so so much.
It might sound silly but I need you to be even more simpler, as I am very naive about these commands. I need like basic instruction.

I have in front of me one windows pc. I downloaded on this pc:
R and various packages included CummeRbund
I dont know how to install cufflinks?I follow the instructions but I don't know even what does it mean "2.Unpack bjam and add it to your PATH"...How do i know which one is my PATH?

Sorry to bother you with such silly questions,but I realy need a step-by-step tutorial. It is just crucial for me to have all this set up sp that I can run the programs.

Hope you can help!
Thanks for yor patience

Irene

[BenS]

Hi Ben, thanks so so much.
It might sound silly but I need you to be even more simpler, as I am very naive about these commands. I need like basic instruction.

I have in front of me one windows pc. I downloaded on this pc:
R and various packages included CummeRbund
I dont know how to install cufflinks?I follow the instructions but I don't know even what does it mean "2.Unpack bjam and add it to your PATH"...How do i know which one is my PATH?

Sorry to bother you with such silly questions,but I realy need a step-by-step tutorial. It is just crucial for me to have all this set up sp that I can run the programs.

Hope you can help!
Thanks for yor patience

Irene

Irene,

Alright, first up, installing cufflinks is a somewhat long process, and it will likely take a while. First of all, if you're working from a PC, you will be installing boost in a slightly different way than what cufflinks describes to say the least. You will want to got to the boost home page and download the windows version of Boost, and the installation process is somewhat different to say the very least. If you would like to install boost (note you can install it using windows and still use it in Cygwin) using Command Prompt (Like I did)

http://www.boost.org/doc/libs/1_50_0/more/getting_started/windows.html

should be a good place to get started, if you would like to install it using Cygwin

http://www.boost.org/doc/libs/1_50_0/more/getting_started/unix-variants.html

will be better. The commands for installing boost on the cufflinks page aren't as practical for a windows user from my experience, so I would mostly use the instructions for installing boost on the boost home page.

Note: assigning your boost path should go something like this:
export BOOST_ROOT=/cygdrive/c/AnalysisTools/boost:$BOOST_ROOT
export PATH=/cygdrive/c/AnalysisTools/boost/bin:$PATH


Next, samtools installation should go almost exactly the same on cygwin as on the cufflinks page. (REMEMBER: you'll need to have installed the proper package to use the make command in Cygwin, since it's not one of the defaults)

Note: adding a line to your path in Cygwin will normally involve doing something link this:
export PATH=/cygdrive/c/AnalysisTools/samtools/samtools:$PATH

Also, for the copying of stuff over to the usr folder, getting to the usr directory is as simple as typing cd /usr

For eigen, the explanation on the cufflinks page is 100% workable with cygwin, just remember that the usr folder is inside whatever folder that you installed Cygwin, and copying the files should go fine. (I attached a picture of where I found it in my computer, and where I copied stuff to)

There are a couple fixes I had to use to even get the cufflinks installation to go as far as it did, http://seqanswers.com/forums/showthread.php?t=16637 has one of them, but I haven't gotten any further than that. The fix seemed to mention that downgrading the boost version could also help, so you may want to look in to that.

I hope this helps, I did this awhile ago so I may be being a bit inaccurate, but I'm piecing together what I can from my Cygwin history.

[IBseq]

Ben thanks again a lot for your patience.

I am honestly lost. Your instruction are very nice but I don't know where to start from. I open command prompt but I did not understand what to type. Or do i have to type on Cywgin?

I am very sorry to bother you with such silly questions but for me it's alien language!!


Thanks again
Irene

[BenS]

Irene,

Whether it is in Cygwin or in Command Prompt, you will need to navigate around and write the correct commands. For instance cd C: in command prompt or cygwin will take you to your c drive location. For instance if boost is in the folder C:\AnalysisTools\boost, in Command Prompt you will need to type cd C:\AnalysisTools\boost , then once you're there you will need to follow these instructions: http://www.boost.org/boost-build2/do...tallation.html .
If your doing it with Cygwin, you would write cd /cygdrive/c/AnalysisTools/boost/ .

For instruction on moving around Cygwin, I'd look at this: http://mally.stanford.edu/~sr/computing/basic-unix.html

For Command Prompt: http://www.computerhope.com/overview.htm .

It doesn't matter what you use to compile/install boost as long as you download the correct files for that interface. If you download the windows files, use Command Prompt, if you download the Unix files, use Cygwin.

Hope this Helps
-Ben

[BenS]

Irene,

I don't know if I can answer your question specifically, but I can give you some links that might help. Basically, the process needed to install boost is right here http://www.boost.org/boost-build2/do...tallation.html . It gives a pretty good explanation. The way to navigate through the command line is http://www.computerhope.com/overview.htm which has most of the major commands you will need to move around in the command line. If you download the windows version of boost, that is what you will need to use. On the other hand, if you download the UNIX version of boost, you will need to use http://mally.stanford.edu/~sr/computing/basic-unix.html commands to move around. Specific commands to install boost are in these three websites for you to set up boost.