Thanks Nate! Updated documentation is always welcome and useful. I appreciate the clarifications.
-J On Mon, Dec 12, 2011 at 10:18 AM, Nate Coraor <n...@bx.psu.edu> wrote: > On Dec 9, 2011, at 4:34 PM, Josh Nielsen wrote: > > > Hello, > > > > I have a question which I have not seen specifically addressed in the > online Galaxy wiki documentation about how to integrate tools > (dependencies) into Galaxy. I have implemented a locally managed instance > of Galaxy that my business is using with our cluster and now have a freshly > installed and configured instance of Galaxy running. It is bare-bones right > now and I did not use mercurial to sync any existing files/directory > structures. I have seen the page on external tool dependencies ( > http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies) needed for > Galaxy, but I am somewhat unsure where to place the tools to utilize them > as intended (other than through trial & error). > > > > It appears that there are shell directories for the tools under > ~/galaxy-dist/tools/ with basic wrapper scripts but without the > corresponding executables (very few that I've noticed have the tools > already in them). Is the intent to download the dependency tools and > (building from source if necessary) take the binaries in those directories > and copy them to their corresponding directory under ~/galaxy-dist/tools/? > This seems to have worked with an error I first got when clipping a FASTQ > file which reported that fastx_clipper was not a recognized command. So I > downloaded the FASTX Toolkit, compiled the binaries, and copied only the > binaries into the corresponding fastx tools directory. Would I do the same > thing for TopHat and Cufflinks by taking all their binaries (combined) and > copying them into ~/galaxy-dist/tools/ngs_rna/? > > Hi Josh, > > There are two ways to do this. The simplest is to place the binaries into > a directory on the Galaxy user's $PATH. The second is via the tool > dependency system, which I need to write up documentation for to put in the > wiki, which I'll do this week. > > > Even if that is the case though, I have occasionally gotten errors about > tools missing in completely different directories. One was for the FASTQ > Groomer. One user saw this error in their browser (which for now is the > only way I know to figure out where tools are *expected* to be): > > > > File "/home/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 141, > in assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot > find executable %s' % opts.executable AssertionError: ##rgFastQC.py error - > cannot find executable > /home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc > > Java JARs are a special case, and FastQC has a unique way of locating its > jars, which is why it is expected to be found in that directory. This > needs to be documented. > > > > > To fix this I downloaded the FastQC tar file from its webpage, unzipped > it, and copied the fastqc binary/script to the > "home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/" directory. I also > had to mkdir FastQC/ under jars/ to place it there since it didn't already > exist. Had I not been told the specific directory by the error I'm not sure > how I would have intuitively known to place the binary there (unless I'm > overlooking some critical documentation). And how do I know that other > similar things are not missing which should be there? Can anyone shed some > light on this please? Adding a brief page on the Galaxy wiki site under the > Admin section about this would really help, even if it only showed an > example for one or two specific tools. > > The list of external dependencies by tool is maintained here: > > http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies > > I'll update this page with links to the new documentation when I write it. > I should also add that work is under way to make it possible to > automatically install these dependencies as needed. > > --nate > > > > > Thanks, > > Josh > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > > > http://lists.bx.psu.edu/ > > -- Josh Nielsen Systems Administrator HudsonAlpha Institute for Biotechnology 256-319-1485
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