Error Locating Program Bowtie-build
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but am getting the following error about not being able to find bowtie: >>python tophat2 example tophat -r 20 test_ref reads_1.fq reads_2.fq [Fri Jun 4 12:53:41 2010]
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Beginning TopHat run (v1.0.11) ----------------------------------------------- [Fri Jun 4 12:53:41 2010] Preparing output location ./tophat_out/ [Fri Jun tophat command line 4 12:53:41 2010] Checking for Bowtie index files [Fri Jun 4 12:53:41 2010] Checking for reference FASTA file [Fri Jun 4 12:53:41 2010] Checking for Bowtie tophat2 tutorial [FAILED] Error: bowtie not found on this system I am working on a Mac OS X machine and am unsure how to specify a "path". I usually place the program in the working directory. In this case, I have a TopHat directory where I've placed everything (the test data, the reference set, the
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TopHat executables, and the bowtie executables): bed_to_juncs juncs_db test_ref.2.ebwt bowtie library_stats test_ref.fa bowtie-build long_spanning_reads test_ref.rev.1.ebwt bowtie-inspect mask_sam test_ref.rev.2.ebwt closure_juncs prep_reads tophat contig_to_chr_coords reads_1.fq tophat_out extract_reads reads_2.fq tophat_reports fix_map_ordering segment_juncs gff_juncs test_ref.1.ebwt Any suggestions for how to get the computer to find Bowtie? Thanks. zorph06-08-2010, 11:45 AMDepending on the shell you're using, you'll be doing the following: • If you are using the Bash shell, you have to edit the ".bashrc" file in your home directory by adding the following two (2) lines of code at the end: o PATH=$PATH:/path/to/bowtie/0.12.5 o export PATH • If you are using the C shell, you have to edit the ".cshrc" file in your home directory by adding the following one (1) line to the end: o set path = (/path/to/bowtie/bowtie/0.12.5 $path) Hope this helps. To make sure it's in your path, you should just be able to type in "Bowtie" and the program should be brought up. Good Luck! albrown41506-08-2010, 12:36 PMThan
faq • rss Community Log In Sign Up Add New Post Question: Execute Tophat Via Java 1 5.3 years ago by Stevelor • 310 Stevelor • 310 wrote: tophat2 download Hi all, I'm trying to run tophat via an Java interface. With other bowtie2 index mapping tools like bowtie etc. it works perfect. If i execute the tophat start command via java runtime exec() it
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doesn't work! But if i copy the command into the shell it works fine...so what is wrong?! Is it becaue of the nested program structure, that java doesn't allow tophat to execute bowtie?? http://seqanswers.com/forums/archive/index.php/t-5427.html Can anyone help me or has experiences about that?? Cheers! Steve tophat java • 1.2k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 5.2 years ago by Ido Tamir ♦ 4.6k • written 5.3 years ago by Stevelor • 310 post the error message that you get ADD REPLY • link written 5.3 years ago https://www.biostars.org/p/10249/ by Istvan Albert ♦♦ 66k 2 5.3 years ago by Pierre Lindenbaum ♦ 86k France Pierre Lindenbaum ♦ 86k wrote: I guess tophat is in your $PATH that's why it runs without any problem with the shell. try to put the full path to the tophat executable in the exec command. ADD COMMENT • link written 5.3 years ago by Pierre Lindenbaum ♦ 86k Tophat actually runs.....but the output stream says: [Fri Jul 15 07:49:32 2011] Beginning TopHat run (v1.3.1) [Fri Jul 15 07:49:32 2011] Preparing output location /home/chg/Desktop/ [Fri Jul 15 07:49:32 2011] Checking for Bowtie index files [Fri Jul 15 07:49:32 2011] Checking for reference FASTA file [Fri Jul 15 07:49:32 2011] Checking for Bowtie Error locating program: bowtie BUT BOWTIE IS IN THE $PATH....ahhh :( ADD REPLY • link written 5.3 years ago by Stevelor • 310 Can you use exec("echo $PATH") to check $PATH of the java can find bowtie? ADD REPLY • link written 5.2 years ago by Ning-Yi Shao • 330 0 5.3 years ago by Ido Tamir ♦ 4.6k Austria Ido Tamir ♦ 4.6k wrote: As others posted without error message its difficult to give advice.[?] a) Recent
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