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Old 11-17-2010, 06:37 AM   #1
jfofly
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Join Date: May 2010
Posts: 9
Default Tophat install problem

Having a problem installing TopHat v.1.1.x onto a PC using cygwin. I have Bowtie 0.12.7 and Samtools 0.1.9 properly (as far as I can tell) installed and configured. Running ./configure for tophat I get :


Quote:
# ./configure --prefix=/path/to/install/directory/
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 build system type... i686-pc-cygwin
checking host system type... i686-pc-cygwin
checking for gcc... gcc
checking for C compiler default output file name... a.exe
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... .exe
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gawk... (cached) gawk
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking for ar... ar
checking for perl... /usr/bin/perl
checking for bash... /usr/bin/bash
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/s
ite-packages
checking for bamlib... yes
checking how to run the C preprocessor... gcc -E
checking for egrep... 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 how to run the C++ preprocessor... g++ -E
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for ANSI C header files... (cached) 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... no
checking for an ANSI C-conforming const... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGE_FILES value needed for large files... no
checking for gzread in -lz... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for memset... yes
checking for strdup... yes
checking for strrchr... yes
checking for strtol... yes
checking for strsep... yes
checking if gcc accepts -m64... yes
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: config.h is unchanged
config.status: executing depfiles commands

-- tophat 1.1.0 Configuration Results --
C compiler: gcc -Wall -m64 -O3 -DNDEBUG
C++ compiler: g++ -Wall -m64 -O3 -DNDEBUG -I/usr/local/include
GCC version: gcc (GCC) 3.4.4 (cygming special, gdc 0.12, using dmd 0.1
25)
Host System type: i686-pc-cygwin
Install prefix: /path/to/install/directory/
Install eprefix: ${prefix}

See config.h for further configuration information.
Email <cole@cs.umd.edu> with questions and bug reports.

Running make I get:

Quote:
# make
make all-recursive
make[1]: Entering directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0'
Making all in src
make[2]: Entering directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0/src
'
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include -Wall -m64 -O3 -DNDEBUG -I
/usr/local/include -I./SeqAn-1.1 -Wall -m64 -O3 -DNDEBUG -I/usr/local/include -
MT reads.o -MD -MP -MF ".deps/reads.Tpo" -c -o reads.o reads.cpp; \
then mv -f ".deps/reads.Tpo" ".deps/reads.Po"; else rm -f ".deps/reads.T
po"; exit 1; fi
reads.cpp:1: sorry, unimplemented: 64-bit mode not compiled in
In file included from reads.cpp:20:
bwt_map.h: In constructor `RefSequenceTable::RefSequenceTable(const std::string&
, bool, bool)':
bwt_map.h:332: warning: comparison between signed and unsigned integer expressio
ns
make[2]: *** [reads.o] Error 1
make[2]: Leaving directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0/src'

make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0'
make: *** [all] Error 2

Any suggestions? I'm relatively new to all this computer stuff, so dumbed down answers would be appreciated. Thanks.
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Old 11-17-2010, 07:41 AM   #2
jmarshall
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Location: Cambridge, UK

Join Date: Jul 2009
Posts: 39
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Code:
checking if gcc accepts -m64... yes
[...]
-- tophat 1.1.0 Configuration Results --
C compiler: gcc -Wall -m64 -O3 -DNDEBUG
C++ compiler: g++ -Wall -m64 -O3 -DNDEBUG -I/usr/local/include
[...]
reads.cpp:1: sorry, unimplemented: 64-bit mode not compiled in
You are suffering from the same problem that the person in this thread was: http://seqanswers.com/forums/showpos...99&postcount=4

I thought that Cole had since fixed this configure bug, but apparently not. In tophat 1.1.4 (it looks like you're using 1.1.3 or so), you should change CFLAGS to CXXFLAGS on line 6670 of tophat-1.1.4/configure and rerun configure. This will hopefully cause different flags to be shown on the "C compiler" and "C++ compiler" lines shown above, and you'll be able to proceed to build a 32-bit version.

(If you were on a Mac, you would want to make the same change on lines 6632 and 6650 too.)
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Old 11-17-2010, 10:25 AM   #3
jfofly
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Location: NC

Join Date: May 2010
Posts: 9
Default

Great. Thanks jmarshall. I had seen that previous thread, but the configure file I had was different and didn't know if there was a specific instance of CFLAGS that needed to be changed. It seems to have installed properly now.

Next issue! When running the test data I get the following error:

Quote:
# tophat -r 20 test_ref reads_1.fq reads_2.fq

[Wed Nov 17 14:09:55 2010] Beginning TopHat run (v1.1.4)
-----------------------------------------------
[Wed Nov 17 14:09:55 2010] Preparing output location ./tophat_out/
[Wed Nov 17 14:09:55 2010] Checking for Bowtie index files
[Wed Nov 17 14:09:55 2010] Checking for reference FASTA file
[Wed Nov 17 14:09:55 2010] Checking for Bowtie
Traceback (most recent call last):
File "/path/to/install/directory/bin/tophat", line 2223, in <module>
sys.exit(main())
File "/path/to/install/directory/bin/tophat", line 2135, in main
check_bowtie()
File "/path/to/install/directory/bin/tophat", line 833, in check_bowtie
bowtie_version = get_bowtie_version()
File "/path/to/install/directory/bin/tophat", line 738, in get_bowtie_version
if len(bowtie_version) == 3:
TypeError: object of type 'NoneType' has no len()
I already have $PATH pointed to the bowtie folder as some previous threads here suggest, and am at a loss as to what else to do.

.....
To anyone having these types of problems on a PC using Cygwin, and are novices like myself...try getting on a Mac. The installation and running of these programs goes a lot smoother!!!

Last edited by jfofly; 12-07-2010 at 12:02 PM. Reason: Problem Solved...Use a Mac!
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Old 01-25-2011, 12:57 PM   #4
limericksean
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Location: NYC

Join Date: Jan 2011
Posts: 4
Default tophat 1.2.0 make error

Hi,
I'm having a similar but different issue. I'm getting a make error installing Tophat 1.2.0 on 32-bit linux (ubuntu 10.04).
Configure is fine but the make returns:


sean@sean:~/Downloads/tophat-1.2.0$ make
make all-recursive
make[1]: Entering directory `/home/sean/Downloads/tophat-1.2.0'
Making all in src
make[2]: Entering directory `/home/sean/Downloads/tophat-1.2.0/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/local/include -Wall -march=i686 -O3 -DNDEBUG -I/usr/local/include -I./SeqAn-1.1 -Wall -march=i686 -O3 -DNDEBUG -I/usr/local/include -MT juncs_db.o -MD -MP -MF ".deps/juncs_db.Tpo" -c -o juncs_db.o juncs_db.cpp; \
then mv -f ".deps/juncs_db.Tpo" ".deps/juncs_db.Po"; else rm -f ".deps/juncs_db.Tpo"; exit 1; fi
In file included from juncs_db.cpp:32:
bwt_map.h: In member function ‘bool HitStream::next_read_hits(HitsForRead&)’:
bwt_map.h:680: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
In file included from ./SeqAn-1.1/seqan/sequence.h:51,
from juncs_db.cpp:26:
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::clear(seqan::String<TValue, TSpec>&) [with TValue = char, TSpec = seqan::CStyle]’:
./SeqAn-1.1/seqan/sequence/string_cstyle.h:492: instantiated from ‘static void seqan::_Assign_String_2_StringArray<TExpand, true>::assign_(seqan::String<char, seqan::CStyle>&, seqan::String<char, TSourceSpec>&) [with TSourceSpec = seqan::Alloc<void>, TExpand = const seqan::Tag<seqan::TagExact_>]’
./SeqAn-1.1/seqan/sequence/string_cstyle.h:522: instantiated from ‘void seqan::assign(seqan::String<TTargetValue, seqan::CStyle>&, seqan::String<TValue, TSpec>&, seqan::Tag<TTag>) [with TValue = char, TSourceSpec = seqan::Alloc<void>, TExpand = seqan::TagExact_]’
./SeqAn-1.1/seqan/sequence/string_base.h:737: instantiated from ‘void seqan::assign(seqan::String<TValue, TSpec>&, TSource&) [with TTargetValue = char, TTargetSpec = seqan::CStyle, TSource = seqan::String<char, seqan::Alloc<void> >]’
./SeqAn-1.1/seqan/sequence/string_cstyle.h:97: instantiated from ‘seqan::String<TTargetValue, seqan::CStyle>::String(TString&) [with TString = seqan::String<char, seqan::Alloc<void> >, TValue = char]’
./SeqAn-1.1/seqan/sequence/string_cstyle.h:798: instantiated from ‘typename seqan::Value<T, 0>::Type* seqan::toCString(T&) [with T = seqan::String<char, seqan::Alloc<void> >]’
juncs_db.cpp:327: instantiated from here
./SeqAn-1.1/seqan/sequence/string_base.h:207: error: no matching function for call to ‘_setLength(seqan::String<char, seqan::CStyle>&, int)’
make[2]: *** [juncs_db.o] Error 1
make[2]: Leaving directory `/home/sean/Downloads/tophat-1.2.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/sean/Downloads/tophat-1.2.0'
make: *** [all] Error 2
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Old 07-17-2013, 11:22 AM   #5
twotwo
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Location: Ohio

Join Date: May 2012
Posts: 40
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Quote:
Originally Posted by jmarshall View Post
Code:
checking if gcc accepts -m64... yes
[...]
-- tophat 1.1.0 Configuration Results --
C compiler: gcc -Wall -m64 -O3 -DNDEBUG
C++ compiler: g++ -Wall -m64 -O3 -DNDEBUG -I/usr/local/include
[...]
reads.cpp:1: sorry, unimplemented: 64-bit mode not compiled in
You are suffering from the same problem that the person in this thread was: http://seqanswers.com/forums/showpos...99&postcount=4

I thought that Cole had since fixed this configure bug, but apparently not. In tophat 1.1.4 (it looks like you're using 1.1.3 or so), you should change CFLAGS to CXXFLAGS on line 6670 of tophat-1.1.4/configure and rerun configure. This will hopefully cause different flags to be shown on the "C compiler" and "C++ compiler" lines shown above, and you'll be able to proceed to build a 32-bit version.

(If you were on a Mac, you would want to make the same change on lines 6632 and 6650 too.)
Hi, I installed the newest tophat 2.0.9. And I have similar problem in configure.


-- tophat 2.0.9 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/home/twotwo/software/boost_154/include -I/home/twotwo/software/samtools-0.1.19/samtools0119/include -I./SeqAn-1.3
Linker flags:
GCC version: gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-54)
Host System type: x86_64-unknown-linux-gnu
Install prefix: /home/twotwo/software/tophat209
Install eprefix: ${prefix}

See config.h for further configuration information.
Email <tophat.cufflinks@gmail.com> with questions and bug reports.


when I ran make, I got the following error:
thread.cpp.text+0x1c84): undefined reference to `clock_gettime'
thread.cpp.text+0x1cfa): undefined reference to `clock_gettime'
thread.cpp.text+0x1d65): undefined reference to `clock_gettime'
thread.cpp.text+0x1dd0): undefined reference to `clock_gettime'
thread.cpp.text+0x1e3b): undefined reference to `clock_gettime'
/home/twotwo/software/boost_154/lib/libboost_thread.a(thread.o):thread.cpp.text+0x1ea6): more undefined references to `clock_gettime' follow
collect2: ld returned 1 exit status
make[2]: *** [segment_juncs] Error 1
make[2]: Leaving directory `/home/twotwo/software/tophat-2.0.9/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/twotwo/software/tophat-2.0.9'
make: *** [all] Error 2

Any comments?
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Old 07-17-2013, 11:32 AM   #6
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,076
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Quote:
Originally Posted by twotwo View Post
Hi, I installed the newest tophat 2.0.9. And I have similar problem in configure.


-- tophat 2.0.9 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/home/twotwo/software/boost_154/include -I/home/twotwo/software/samtools-0.1.19/samtools0119/include -I./SeqAn-1.3
Linker flags:
GCC version: gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-54)
Host System type: x86_64-unknown-linux-gnu
Install prefix: /home/twotwo/software/tophat209
Install eprefix: ${prefix}

See config.h for further configuration information.
Email <tophat.cufflinks@gmail.com> with questions and bug reports.


when I ran make, I got the following error:
thread.cpp.text+0x1c84): undefined reference to `clock_gettime'
thread.cpp.text+0x1cfa): undefined reference to `clock_gettime'
thread.cpp.text+0x1d65): undefined reference to `clock_gettime'
thread.cpp.text+0x1dd0): undefined reference to `clock_gettime'
thread.cpp.text+0x1e3b): undefined reference to `clock_gettime'
/home/twotwo/software/boost_154/lib/libboost_thread.a(thread.o):thread.cpp.text+0x1ea6): more undefined references to `clock_gettime' follow
collect2: ld returned 1 exit status
make[2]: *** [segment_juncs] Error 1
make[2]: Leaving directory `/home/twotwo/software/tophat-2.0.9/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/twotwo/software/tophat-2.0.9'
make: *** [all] Error 2

Any comments?
Try the suggestion in post #9: http://seqanswers.com/forums/showthread.php?t=28225
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Old 07-17-2013, 11:54 AM   #7
twotwo
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Location: Ohio

Join Date: May 2012
Posts: 40
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Quote:
Originally Posted by GenoMax View Post
great! Thanks!
Here is my code. It really works.
./configure LIBS=-lrt --prefix=/home/twotwo/software/tophat209 --with-boost=/home/twotwo/software/boost_154 --with-bam=/home/twotwo/software/samtools-0.1.19/samtools0119
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