Hi Doris,

The repository was updated in October with the fix for the dependency path.
Please let us know if this fixes it for you.

--nate

On Mon, Feb 2, 2015 at 1:52 PM, Sajdak, Doris <dj...@buffalo.edu> wrote:

>  I’m still in a holding pattern on these Miller Lab tools.  Has anyone
> responded to your requests from back in September?  I emailed them in
> August as well and heard nothing.  We have users at our university that
> want to use these tools on our Galaxy instance.  If there is no way to get
> them to change it in the tool shed, is there a way I can install quicktree
> myself and then tell Galaxy the dependency is installed for the other
> Miller Lab tools?
>
>
>
> Thank you for any help you can provide.
>
>
>
> *From:* Nate Coraor [mailto:n...@bx.psu.edu]
> *Sent:* Wednesday, September 24, 2014 2:58 PM
> *To:* Will Holtz
> *Cc:* Sajdak, Doris; galaxy-...@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] problems installing tool dependency
>
>
>
> I've just looked at this as well, it appears that /pub4 is not exposed and
> does not allow you to change into it, but it does allow you to fetch if you
> request files under it via the full path.
>
>
>
> e.g.:
>
>
>
> nate@victory% ncftp ftp.sanger.ac.uk
>
> ...
>
> Logged in to ftp.sanger.ac.uk.
>
> ncftp / > ls
>
> ls-lR.gz                        .ok_to_rsync                    README
>                      .request-for-update.lock
>
> .message                        pub/
>  .request-for-update
>
> ncftp / > cd pub4
>
> Could not chdir to pub4: server said: pub4: No such file or directory
>
> ncftp / > cd /pub4
>
> Could not chdir to /pub4: server said: pub4: No such file or directory
>
> ncftp / > get /pub4/resources/software/quicktree/quicktree.tar.gz
>
> quicktree.tar.gz:                                       38.12 kB  124.19
> kB/s
>
> ncftp / >
>
>
>
> I'll contact some folks in the Miller Lab to see if the tool can be
> updated to the path under /pub.
>
>
>
> On Wed, Sep 24, 2014 at 2:09 PM, Will Holtz <who...@lygos.com> wrote:
>
>  I also was able to download quicktree.tar.gz by clicking on the URL in
> your message. However, when I manually ftp into ftp.sanger.ac.uk, there
> is no /pub4 directory. I'm a bit confused about how those two statements
> are both true, but maybe it will help someone else figure this out.
> Removing the '4' does result in a valid path (
> ftp://ftp.sanger.ac.uk/pub/resources/software/quicktree/quicktree.tar.gz).
>
> -Will
>
>
>
> On Wed, Sep 24, 2014 at 10:57 AM, Sajdak, Doris <dj...@buffalo.edu> wrote:
>
>   Hi all,
>
>
>
> I am trying to install the Genome Diversity tools from the Miller Lab that
> are in the Galaxy toolshed.  I’ve been able to get all dependencies
> installed except Quicktree.  Whenever I try to install it, I get the error:
>
>
>
> Error downloading from URL
>
> ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz:
>
> <urlopen error ftp error: 550 pub4: No such file or directory>
>
>
>
> This is the tool_dependencies.xml file for installing quicktree:
>
>
>
> <?xml version="1.0"?>
>
> <tool_dependency>
>
>   <package name="quicktree" version="1.1">
>
>     <install version="1.0">
>
>       <actions>
>
>         <!-- Download source code -->
>
>         <action type="download_by_url"
> target_filename="quicktree_1.1.tar.gz">
> ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz
> </action>
>
>
>
>         <!-- Build quicktree -->
>
>         <action type="shell_command">make quicktree</action>
>
>
>
>         <!-- Install quicktree -->
>
>         <action type="shell_command">cp -R bin $INSTALL_DIR</action>
>
>
>
>         <!-- Set environment for dependent repositories -->
>
>         <action type="set_environment">
>
>           <environment_variable name="PATH"
> action="prepend_to">$INSTALL_DIR/bin</environment_variable>
>
>         </action>
>
>       </actions>
>
>     </install>
>
>   </package>
>
> </tool_dependency>
>
>
>
>
>
> I know this is not their file I’m downloading but the thing is, if I copy
> and paste the URL, I can download it with no problem.  I’m not sure why
> it’s reporting that it can’t be found but the xml looks right to me.  I’ve
> tried contacting the Miller Lab about this but haven’t heard from anyone so
> I’m hoping someone here can tell me how to move past this problem.  Is
> there a way to install this tool manually and have the main Genome
> Diversity tools recognize it on the Galaxy server?
>
>
>
> Also, I noticed when looking at the Tool Dependency Definitions at
> https://toolshed.g2.bx.psu.edu/ there are errors going back many versions
> for this tool (see Test runs – Installation errors – Tool dependencies).
>
>
>
> Thank you for any help you can provide.
>
>
>
> Dori
>
>
>
> **********************************
>
> Dori Sajdak
>
> Senior Systems Administrator
>
> State University of NY at Buffalo
>
> Center for Computational Research
>
> 701 Ellicott St
>
> Buffalo, NY 14203
>
> Phone: (716) 881-8934
>
> Fax: (716) 849-6656
>
> Web: http://ccr.buffalo.edu
>
> **********************************
>
>
>
>
>
>
>
>
>
> ___________________________________________________________
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> ___________________________________________________________
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>
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