Confusing Requirements for BiblioSpec Compilation

[proteowizard]

Confusing Requirements for BiblioSpec Compilation

[chambm]

Sorry for the confusion. Did you clone with git or downloaded it some other way? If so, try the master branch (it's the git equivalent of trunk).

[DarioS]

I downloaded master and I get

fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

I'm not sure why it has to be a git repository. The instructions state "Download (or clone with git) the trunk/pwiz directory from the ProteoWizard git repository." So, it seems that git clone is optional. I clicked the Download ZIP button and used unzip to decompress it which seems to be acceptable, according to the instructions. Also, should it be necessary for users to download all 631 MB of ProteoWizard just to compile the BiblioSpec spectral library file format converter? It doesn't seem modular. Are Ubuntu DEBs of it available from somewhere?

[chambm]

We recently switched from SVN to Git and there have been growing pains. The need to get the branch and revision info via the git command rather than through SVN properties is one of them. The BiblioSpec build documentation has only been lightly updated to reflect this transition. Here's a diff that will make the git commands optional (I will get this integrated into master soon):
https://gist.github.com/chambm/bc6e370dd490ed491723a56039969fd0

Here's a subset source tarball which should only contain the files necessary to build BiblioSpec:
http://teamcity.labkey.org/viewLog.html?buildId=576515&tab=artifacts&buildTypeId=BiblioSpecSubsetSourceTarball&guest=1
The without-t version omits test files to save space.

But yes, BiblioSpec is not a standalone application. It depends on ProteoWizard for reading some of the file types it supports.

[chambm]

@DarioS let me know if this works for you so I can close the issue. Thanks.

[DarioS]

I downloaded bibliospec-src-without-t-3_0.tar.bz2 from the TeamCity website, extracted it and ran quickbuild.sh but the error remains the same:

fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

I was planning to wait a few days and download ProteoWizard again once the Gist was incorporated into the repository.

[chambm]

OK latest master has the diff I posted above. #50