sharpton
Installation Issue
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.
- 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.
- 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
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 [email protected] 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.
- 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.
- 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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Thomas J. Sharpton
Assistant Professor Department of Microbiology Department of Statistics Oregon State University
(541) 737-8623 [email protected] @tjsharpton lab.sharpton.org
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
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 [email protected] 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
— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/sharpton/shotmap/issues/6#issuecomment-210102227
Thomas J. Sharpton
Assistant Professor Department of Microbiology Department of Statistics Oregon State University
(541) 737-8623 [email protected] @tjsharpton lab.sharpton.org
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