On Mon, Feb 2, 2015 at 1:52 PM, Sajdak, Doris <djm29@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:nate@bx.psu.edu]
Sent: Wednesday, September 24, 2014 2:58 PM
To: Will Holtz
Cc: Sajdak, Doris; galaxy-dev@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 <wholtz@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 <djm29@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>

        

        <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>

        

        <action type="shell_command">make quicktree</action>

        

        <action type="shell_command">cp -R bin $INSTALL_DIR</action>

        

        <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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