Error Locating Program Samtools
Contents |
• rss Community Log In Sign Up Add New Post Question: Tophat 0 5.2 years ago by Luciano samtools question Cosme • 220 Luciano Cosme • 220 wrote: Hi, I am
Galaxy Samtools
running galaxy locally and when I perform alignments with TopHat I get the following error: Error in tophat: [Fri Jul 29 17:55:47 2011] Beginning TopHat run (v1.3.1) [Fri Jul 29 17:55:47 2011] Preparing output location ./tophat_out/ [Fri Jul 29 17:55:47 2011] Checking for Bowtie index files [Fri Jul 29 17:55:47 2011] Checking for reference FASTA file Warning: Could not find FASTA file /tmp/tmp1dXHLG/dataset_26.dat.fa [Fri Jul 29 17:55:47 2011] Reconstituting reference FASTA file from Bowtie index Executing: /bin/bowtie-inspect /tmp/tmp1dXHLG/dataset_26.dat > ./tophat_out/tmp/dataset_26.dat.fa [Fri Jul 29 17:56:39 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Fri Jul 29 17:56:39 2011] Checking for Samtools Error locating program: samtools I installed the samtools (in several places already), but it seems I did not put it in the right place. So where galaxy search for it? Thank you. Luciano alignment bowtie samtools bam • 738 views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 5.2 years ago by Jennifer Hillman Jackson ♦ 20k • written 5.2 years ago by Luciano Cosme • 220 0 5.2 years ago by Jennifer Hillman Jackson ♦ 20k United States Jennifer Hillman Jackson ♦ 20k wrote: Hello Luciano, Here are is the core wiki link to help with NGS tools (including SamTools) set up and installation. http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup For next time, the galaxy-dev@bx.psu.edu mailing list would be the best place to send new questions or even follow-up questions to this one if problems persist. The development community can be very helpful in sorting out local installation issue that may come up. Subscribing may also be of interest: http://lists.bx.psu.edu/listinfo/galaxy-dev http://galaxyproject.org/Supp
[ date ] [ thread ] [ subject ] [ author ] Looks like the "development" package for zlib is missing. Rather than building SAMtools from source, you may want to check if there is a packaged version for your Linux distribution. The package manager [apt-get on Ubuntu(?); I'm on CentOS and use yum] should handle bringing in any dependencies if they are not already installed. If you do indeed want to build from source, use your package manager to install the needed dependency, typically something like zlib-devel. -- Olen On Mon, Aug 1, 2011 at 13:53, Luciano Cosme
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: Hi all, I'm trying to run https://www.biostars.org/p/10249/ tophat via an Java interface. With other mapping tools like bowtie etc. it works perfect. If i execute the tophat start command via java runtime exec() it 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?? Can anyone help me or has experiences about that?? Cheers! Steve error locating 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 by Istvan Albert ♦♦ 66k 2 5.3 years ago by Pierre Lindenbaum ♦ 86k France Pierre Lindenbaum error locating program ♦ 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 versions of tophat also need bowtie and samtools in the path. You have to add the path to them to the environment when you execute the call to tophat. Although by default the subproc