Installation Issue

[amorendt]

HI, I am working to install shotmap for a user at the Researching Computing Center on a CentOS6.6 system and running into two issues in the automated installation via install.pl that I am trying to manually resolve.

1. XML::Tidy gives an error:
   --> Working on XML::Tidy
   Fetching http://www.cpan.org/authors/id/P/PI/PIP/XML-Tidy-1.12.B55J2qn.tgz ... OK
   Configuring XML-Tidy-1.12.B55J2qn ... OK
   Building and testing XML-Tidy-1.12.B55J2qn ... FAIL

Down the road the user finds that the perl script ext/bin/xmltidy does not exist. What are there steps to manually add this perl module within the shotmap package?
Is there an easy way to use an existing perl installation that has all of the required modules instead of having shotmap install its own copy?

Based on adding this module to our stand alone perl installation, this is a testing failure, and so we had to do a hand installation instead of the cpan one.

2. Issue with hmmer:
   --2016-04-06 12:40:40-- ftp://selab.janelia.org/pub/software/hmmer3/3.1b1/hmmer-3.1b1-linux-intel-x86_64.tar.gz
   => “hmmer-3.1b1-linux-intel-x86_64.tar.gz�
   Resolving selab.janelia.org... 206.241.0.22
   Connecting to selab.janelia.org|206.241.0.22|:21... failed: Connection timed out.
   Retrying..

This I was able to resolve by getting the download from http://hmmer.org/download.html, installing, and adding links in the bin directory (at least I hope this will work)

Thanks in advance

Anita

[sharpton]

Hi Anita,

Thanks for your note. Please see my comments below.

Regarding point (1): We are currently working on some changes to the
software that will allow users to point shotmap to their own dependency
install locations. For now, I would recommend creating a symlink to your
installation of xmltidy in the following location:

${SHOTMAP_LOCAL}/ext/bin

For example:

ln -s <path_to_xmltidy> ${SHOTMAP_LOCAL}/ext/bin/

Regarding point (2): The odds are good that you will not end up needing
HMMER, unless the user is specifically invoking the algorithm at runtime
using --search-method hmmsearch or --search-method hmmscan. The default is
to rely on rapsearch. That said, placing symlinks in the following location
(note the difference in path from the above):

${SHOTMAP_LOCAL/bin/hmmscan

${SHOTMAP_LOCAL/bin/hmmsearch

Should work for you.

Please let me know if you have any questions about the above. I'm happy to
help.

Best,

Tom

On Thu, Apr 7, 2016 at 4:26 PM, amorendt notifications@github.com wrote:

HI, I am working to install shotmap for a user at the Researching
Computing Center on a CentOS6.6 system and running into two issues in the
automated installation via install.pl that I am trying to manually
resolve.

1. XML::Tidy gives an error:
   --> Working on XML::Tidy
   Fetching http://www.cpan.org/authors/id/P/PI/PIP/XML-Tidy-1.12.B55J2qn.tgz
   ... OK
   Configuring XML-Tidy-1.12.B55J2qn ... OK
   Building and testing XML-Tidy-1.12.B55J2qn ... FAIL

Down the road the user finds that the perl script ext/bin/xmltidy does not
exist. What are there steps to manually add this perl module within the
shotmap package?
Is there an easy way to use an existing perl installation that has all of
the required modules instead of having shotmap install its own copy?

Based on adding this module to our stand alone perl installation, this is
a testing failure, and so we had to do a hand installation instead of the
cpan one.

2. Issue with hmmer:
   --2016-04-06 12:40:40--
   ftp://selab.janelia.org/pub/software/hmmer3/3.1b1/hmmer-3.1b1-linux-intel-x86_64.tar.gz
   => “hmmer-3.1b1-linux-intel-x86_64.tar.gz�
   Resolving selab.janelia.org... 206.241.0.22
   Connecting to selab.janelia.org|206.241.0.22|:21... failed: Connection
   timed out.
   Retrying..

This I was able to resolve by getting the download from
http://hmmer.org/download.html, installing, and adding links in the bin
directory (at least I hope this will work)

Thanks in advance

Anita

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#6

Thomas J. Sharpton

Assistant Professor
Department of Microbiology
Department of Statistics
Oregon State University

(541) 737-8623
thomas.sharpton@gmail.com
@tjsharpton
lab.sharpton.org

[amorendt]

Thanks Tom, Adding in the link to the xmltidy of our external perl module installation solved the issue and the user is now proceeding with using shotmap. Being able to utilize existing external perl and R installations sounds good.

Anita

[sharpton]

Thanks, Anita. For my information, do you mind passing along any error logs
you received during installation of shotmap and its dependencies? This may
help improve efforts to automate installation for other users.

Best,
Tom

On Thu, Apr 14, 2016 at 12:03 PM, amorendt notifications@github.com wrote:

Thanks Tom, Adding in the link to the xmltidy of our external perl module
installation solved the issue and the user is now proceeding with using
shotmap. Being able to utilize existing external perl and R installations
sounds good.

Anita

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#6 (comment)

Thomas J. Sharpton

Assistant Professor
Department of Microbiology
Department of Statistics
Oregon State University

(541) 737-8623
thomas.sharpton@gmail.com
@tjsharpton
lab.sharpton.org

[amorendt]

Tom, I only have what I had pasted in the initial question. Would you like me to redo the install to generate additional information?

Anita