The pipeline isn't working even after install dependencies

[gearhq]

Hi!

I'm trying to annotate a new Saccharomyces cerevisiae strain with your program but it didn't work. While trying to make it work I noticed some problems through the program files:

• In file "configs.cf" these variables are no listed in INSTALL.txt:

1. SNAP
2. GeneMark and genemark_mod
3. BWA
4. BEDTOOLS
5. SAMTOOLS

However I have these tools installed on my computer and set the path for them.

• When I execute the file agape_annot.sh:
• Got error in line 32 a "fi" was commented with "#"
• After remove the “#” faSize was required at axtChainNet path, but faSize was not present neitheir at axtChainNet version available to download nor in agape binaries folder.
• gff2zff also seems to be necessary, but I couldn’t find it in install instructions neither agape binaries folder.

I looked for the two programs that were missing on the internet but as there is no mention of them in the installation notes, so I'm not sure if they are the correct versions.

Finally, the files adjust_annot.sh, run_agape_assembly.sh, run_AGAPE.sh and run_hugeseq.sh have fixed variables with the path "/srv/gs1/projects/cherry/giltae/AGAPE". Even after changing these variables to directories on my computer, there are dependency problems.

Some programs with huge number of dependencies, like Maker, have specialized scrips to install their dependencies. Do you have something like this to install your pipeline or do you plan to add a server to execute it?

[kastman]

+1 for this. @gtsong your pipeline looks thoughtfully put together, but the code here isn't usable right now (hardcoded paths, cluster submissions, etc.). I'm commenting to get a notice if you decide to re-work it into something more portable. Thanks!