MPA portable requirements and xtandem path
bernt-matthias opened this issue · 0 comments
Dear MPA developers @thilus @tivdnbos,
I'm working on the mpa-portable bioconda recipe and wonder if it is possible to replace the precompiled versions of X!Tandem and Comet (and maybe also MSGF+). In other words I'm looking for a way to configure where the MPA is looking for the binaries.
Seems that MPA includes
- tandem 2015.12.15.2
- Comet version "2016.01 rev. 2"
- MS-GF+ Beta (v9979)
In bioconda currently the following versions are available:
- tandem 15.12.15.2
- Comet 2016013 - 2019015
- msgf_plus: 2016.10.26 - 2020.08.05-0
So except for MSGF+ the exact versions seem to be available. But maybe also using a newer version is possible.
The second problem is that MPA writes the input (xml) files for tandem to the path where the tandem binary is located. Which will fail for multi user installations and is not possible if MPA is used in a container. Can this path be configured?
Could you be so nice to explain the difference between the version numbers of the portable and the server variant?
Lastly, I would like to ask if it is possible to remove the ! from path names. Since ! has a special meaning in bash this creates all sorts of problems