Nate,

I apologize for taking so long to get back to you but I finally revisited this 
today.  I am on the latest Galaxy version (updated this morning) and am still 
having trouble getting this installed.  Is there a way to force an update on 
the tool shed that I may be missing?  The latest update for Genome Diversity in 
my tool shed is showing revision 38 (2014-02-28).  Once the install fails, I go 
to the Genome Diversity repository and click Get Repository Updates (under 
Repository actions) but it says the repository is current and there are no 
updates available.

Sorry these are most likely basic Galaxy questions but we haven’t had a problem 
installing from the tool shed before.

Thank you in advance for your help.

Dori


From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Tuesday, February 03, 2015 9:50 AM
To: Sajdak, Doris
Cc: galaxy-...@lists.bx.psu.edu<mailto:galaxy-...@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] problems installing tool dependency

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<mailto: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<mailto:n...@bx.psu.edu>]
Sent: Wednesday, September 24, 2014 2:58 PM
To: Will Holtz
Cc: Sajdak, Doris; 
galaxy-...@lists.bx.psu.edu<mailto: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<http://ftp.sanger.ac.uk>
...
Logged in to ftp.sanger.ac.uk<http://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<mailto: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<http://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<mailto: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<tel:%28716%29%20881-8934>
Fax: (716) 849-6656<tel:%28716%29%20849-6656>
Web: http://ccr.buffalo.edu
**********************************




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