Platform Specific Issues

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This section deals with problems that one may encounter when installing GEP packages in different system environments. Please contribute any tips and hints on installing packages in a variety of *NIX and Mac environments.

Finishing Issues

Installing phred, phrap, consed

  • Mac OS 10.3, 10.4 PPC

For installation on PPC based mac's running either 10.3 or 10.4 read the information posted here. You will need to contact Chris Shaffer by email at shaffer 'at' biology 'dot' wustl 'dot' edu to obtain a password to download the installation package.

  • Mac OS 10.4 Intel
  • Solaris
  • Linux

Consed Issues

File not found

End line problems

Consed at times has problems finding or reading text files (also know as ASCII files) that do indeed exist and are in the correct place. The problem is often that the file has the wrong end lines. Since Consed is a unix based program it will often not be able to read mac or MS-DOS based text files. This problem occurs most often when students use a mac or PC based program to create a text file that they wish to use with Consed. To avoid this students should either use a unix based program to create the text files or use the flip utility to change the text file to a unix based one. The flip utility allows users to test a file as to its type and, if necessary, change it to a "unix" type for use with consed. See the flip page for more information on how to use this utility.

Spaces in folder names

Another common problem is that consed cannot handle files if there are any spaces in the names of any folders along the path to the file.

You may get an error that looks like this:

Something went wrong running /usr/local/genome/bin/addReads2Consed.perl

M_BB0112A10.fasta.screen.ace.Bio4342.1 /Users/chris/Desktop/gep files/M_BB0112A10/edit_dir/reads_to_raid.fof addReadsAlignments131021. Gave error code 65280 which means Unknown error: 65280

Note the space in the path "/gep files/" this will cause consed to fail. To avoid this issue do not use spaces in the names of any folder along the path to any files that you might want to use with consed.