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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