tophat installation help, beginner

[NotFunny]

Hi I'm hoping someone can help me trouble shoot this.

I installed bowtie, samtool, boost and tophat as suggested on http://ccb.jhu.edu/software/tophat/tutorial.shtml. Everything went well, but when I run the test, I got the following error message. I guess something is run with the Samtools? but I'm not sure what the issue is. I searched previous posts regarding tophat installation but none seems to help. I'd really appreciate any help.



[2014-09-12 17:29:53] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2014-09-12 17:29:53] Checking for Bowtie
Bowtie version: 2.2.3.0
[2014-09-12 17:29:53] Checking for Samtools
Traceback (most recent call last):
File "/Users/xx/bin/tophat", line 4087, in <module>
sys.exit(main())
File "/Users/xx/bin/tophat", line 3885, in main
check_samtools()
File "/Users/xx/bin/tophat", line 1559, in check_samtools
samtools_version_str, samtools_version_arr = get_samtools_version()
File "/Users/xx/bin/tophat", line 1541, in get_samtools_version
samtools_version_arr = [int(version_match.group(x)) for x in [1,2,3]]
AttributeError: 'NoneType' object has no attribute 'group'

[alex_log]

I have similar troubles running tophat 2.0.12 under Ubuntu 14.04.1:

tophat -p 16 -G genes.gtf -o M1_R1_thout genome SRR452328_forward_paired.fq.gz SRR452328_reverse_paired.fq.gz

[2014-09-12 13:01:39] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2014-09-12 13:01:39] Checking for Bowtie
Bowtie version: 2.2.3.0
[2014-09-12 13:01:39] Checking for Samtools
Traceback (most recent call last):
File "/home/alex/bin/tophat", line 4087, in <module>
sys.exit(main())
File "/home/alex/bin/tophat", line 3885, in main
check_samtools()
File "/home/alex/bin/tophat", line 1559, in check_samtools
samtools_version_str, samtools_version_arr = get_samtools_version()
File "/home/alex/bin/tophat", line 1541, in get_samtools_version
samtools_version_arr = [int(version_match.group(x)) for x in [1,2,3]]
AttributeError: 'NoneType' object has no attribute 'group'
alex@alex-Precision-T7600:~/Amin/sra_files$ tophat -p 16 -G genes.gtf -o M1_R1_thout genome SRR452328_forward_paired.fq.gz

First thought was that possibly something wrong with my data. Then I used reads files from test_data but it resulted in similar error message:

#http://ccb.jhu.edu/software/tophat/tutorial.shtml

tophat -r 20 test_ref reads_1.fq reads_2.fq

[2014-09-12 21:57:52] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2014-09-12 21:57:52] Checking for Bowtie
Bowtie version: 2.2.3.0
[2014-09-12 21:57:52] Checking for Samtools
Traceback (most recent call last):
File "/home/alex/bin/tophat", line 4087, in <module>
sys.exit(main())
File "/home/alex/bin/tophat", line 3885, in main
check_samtools()
File "/home/alex/bin/tophat", line 1559, in check_samtools
samtools_version_str, samtools_version_arr = get_samtools_version()
File "/home/alex/bin/tophat", line 1541, in get_samtools_version
samtools_version_arr = [int(version_match.group(x)) for x in [1,2,3]]
AttributeError: 'NoneType' object has no attribute 'group'

Samtools version was not printed out... I applied the new 1.0 release ... Possibly something wrong with the binary... I have tried samtools-0.1.19 but it resulted in the same error message.
Dear bioinformatics community, please help to fix it.

[Cytosine]

Your tophat compilation went without any problems? It should notify you at that point if it cannot find samtools.

Try doing a clean reinstall and note any logged warnings or errors being reported by the following commands:

./configure --prefix=/path/to/tophat_base_dir --with-boost=/path/to/boost_prefix_dir \
 --with-bam=/path/to/libbam_prefix_dir

make

Post logs of those so we get a better idea what is going on.

[NotFunny]

Thanks for the reply. I installed the binary tophat file, so there was no complain. However, when I tried to use the source file to build tophat, there was some complaining about something like can't find the bam files. I did give the correct directories when using the configure command. I'll need to redo this to give you the exact error message. In the meanwhile any suggestion is appreciated.

[NotFunny]

Update: This is what I tried. I downloaded the tophat source file, and tried the following command, as I put everything in the $HOME/bin folder.

./configure --prefix=$HOME/bin --with-boost=$HOME/bin --with-bam=$HOME/bin

I got the following error:

checking for bamlib... configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option.

I also double checked, and seems all files are where they're supposed to be.

Any help is greatly appreciated.

[GenoMax]

Have you installed SAMTools following the directions found here: http://ccb.jhu.edu/software/tophat/tutorial.shtml There is a section on copying libbam.a and the header files to a specific directory on your computer.

[NotFunny]

Yes, I did that. I also verified that the files on in the correct folders. In my case it's $HOME/bin/lib and $HOME/bin/include/bam.

Have you installed SAMTools following the directions found here: http://ccb.jhu.edu/software/tophat/tutorial.shtml There is a section on copying libbam.a and the header files to a specific directory on your computer.

[GenoMax]

Have you tried to provide actual paths (instead of just $HOME). TopHat may not be correctly expanding $HOME.

[muenster]

I could solve the problem compiling the samtools with CFLAGS=-fPIC on fedora20

cd samtools-0.1.19
make CFLAGS=-fPIC

afterwards copying samtools and misc/* bcftools/bcftools to a bin in your $PATH