Doug Senalik's Blog — Things that aren't on the internet yet

Another post in the series of "things that are not on the internet yet", How to install Sequin on Fedora 15, 64-bit

The Sequin home page is http://www.ncbi.nlm.nih.gov/Sequin/download/seq_unix_download.html

Download Sequin, and uncompress it

[user@host programinstallers]$ wget -N ftp://ftp.ncbi.nih.gov/sequin/CURRENT/sequin.linux-x86.tar.gz

Warning, this archive is a tar bomb, it will extract into the current directory

[user@host programinstallers]$ mkdir /usr/local/bin/sequin
[user@host programinstallers]$ cd /usr/local/bin/sequin
[user@host sequin]$ tar -zxvf /programinstallers/sequin.linux-x86.tar.gz

Modify the default PATH so that the program is accessible to all users

[user@host sequin]$ sudo nano /etc/profile
…
PATH="$PATH:/usr/local/bin/sequin"
…

It doesn't work! See this error message when trying to run sequin

[user@host sequin]$ ./sequin
sequin: error while loading shared libraries: libXm.so.3: cannot open shared object file: No such file or directory

And this library is not in the default repositories:

[user@host sequin]$ yum provides 'libXm.so.3'
Loaded plugins: langpacks, presto, refresh-packagekit
No Matches found

We have to install the 32-bit version from the package openmotif, and since it is one version newer, make a symbolic link. But this package is not in the usual repositories, we need to add the rpmfusion repository.

[user@host sequin]$ sudo yum localinstall --nogpgcheck http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-stable... http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-...
…
Installed:
  rpmfusion-free-release.noarch 0:13-4
  rpmfusion-nonfree-release.noarch 0:13-4
[user@host sequin]$ sudo yum install openmotif.i686
…
Installed:
  openmotif.i686 0:2.3.3-1.fc14

Dependency Installed:
  libXp.i686 0:1.0.0-16.fc15

[user@host sequin]$ sudo ln -s /usr/lib/openmotif/libXm.so.4 /usr/lib/libXm.so.3

In case it helps anyone else, to install the Roche 454 sequence analysis software (gsAssembler or newbler, gsMapper, etc.) on a computer running 64 bit Fedora 15, there were a few libraries that needed to be installed first, but a necessary condition to get this to work for me was to first enable both the "updates" and "updates-testing" repositories. This is done using
Applications → System Tools → Add/Remove Software → System → Software Sources → Software Sources

Then, this command installed the necessary libraries, along with a number of dependencies:

sudo yum install zlib.i686 libXi.i686 libXtst.i686 libXaw.i686

The install then went smoothly.
However, the "454 Sequencing Applications" menu did not appear in the main Applications menu. To make them show up (and I am operating in "Fallback mode" if that makes a difference), I also needed this command

sudo ln -s /etc/xdg/menus/applications-merged /etc/xdg/menus/applications-gnome-merged

For reference, here is the error I received before enabling all repositories:

Error: Protected multilib versions: libgcc-4.6.0-10.fc15.i686 != libgcc-4.6.1-9.fc15.x86_64

I am posting this in case it happens a THIRD time and google will then lead me here (hopefully).

A new gbrowse database I was setting up shows only a big red "Not Found" error. Not helpful.

Apache log shows lines like:

[Mon Mar 14 10:00:09 2011] [error] [client 128.128.128.128] indexing was interrupted, so unlinking /var/www/html/gbrowse2/databases/dbnamehere/directory.index at /usr/local/share/perl5/Bio/DB/Fasta.pm line 1053., referer: http://cranberry.vcru.wisc.edu:7280/cgi-gb/gbrowse/mynewdbnamehere/

Still not so helpful.
I made a short Perl program with just this essential part:

use Bio::DB::Fasta;
  my $db      = Bio::DB::Fasta->new('/var/www/html/gbrowse2/databases/mynewdbnamehere');

This gave useful error messages!

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Each line of the fasta entry must be the same length except the last.
    Line above #1682 '
..' is 19 != 52 chars.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368
STACK: Bio::DB::Fasta::calculate_offsets /usr/local/share/perl5/Bio/DB/Fasta.pm:770
STACK: Bio::DB::Fasta::index_dir /usr/local/share/perl5/Bio/DB/Fasta.pm:593
STACK: Bio::DB::Fasta::new /usr/local/share/perl5/Bio/DB/Fasta.pm:488
STACK: ./test.pl:11
-----------------------------------------------------------
indexing was interrupted, so unlinking /var/www/html/gbrowse2/databases/cucumbermito/directory.index at /usr/local/share/perl5/Bio/DB/Fasta.pm line 1053.

So, the actual problem was that the FASTA file had lines of different lengths! Fixed that and the problem is gone.