Hi Kenneth, Thanks a lot. I have opened an issue with the developers of the software who kept that in for developement, and they said they will fix it in their next release.
Regards, Niek On Wed, Jun 15, 2016 at 1:37 PM, Kenneth Hoste <[email protected]> wrote: > Hi Niek, > > I've issued a PR to make the Binary (and MakeCp) easyblock aware of the > general 'keepsymlinks' easyconfig parameter ( > https://github.com/hpcugent/easybuild-easyblocks/pull/959), so with this > in place you should be able to fix your problem by including this in your > easyconfig file: > > keepsymlinks = True > > That does leave the question whether it makes sense to leave broken > symlinks in place though... > > > regards, > > Kenneth > > > On 14/06/16 22:05, Kenneth Hoste wrote: > >> Hi Niek, >> >> Basically, the tarball is broken, is contains a bunch of broken symlinks, >> for example: >> >> $ ls -l db/test/microbiome/bacteria/ >> total 0 >> lrwxrwxrwx 1 vsc40023 vsc40023 50 Jun 14 21:17 bacteria.00.idx -> >> /u/home/s/serghei/project/Bacteria/bacteria.00.idx >> lrwxrwxrwx 1 vsc40023 vsc40023 50 Jun 14 21:17 bacteria.00.nhd -> >> /u/home/s/serghei/project/Bacteria/bacteria.00.nhd >> lrwxrwxrwx 1 vsc40023 vsc40023 50 Jun 14 21:17 bacteria.00.nhi -> >> /u/home/s/serghei/project/Bacteria/bacteria.00.nhi >> >> >> The can also be considered a bug in the Binary easyblock (which is >> leveraged by PackagedBinary you are using), since it should be calling >> copytree with symlinks=True to make it preserve symlinks rather than >> resolve them (cfr. >> https://docs.python.org/2/library/shutil.html#shutil.copytree). >> With that setting, it will happily copy the broken symlinks... >> >> >> regards, >> >> Kenneth >> >> On 13/06/16 18:49, Niek de Klein wrote: >> >>> Hi all, >>> >>> I am trying to install ROP from here: >>> https://github.com/smangul1/rop/archive/1.0.2.tar.gz. I attached the >>> .eb file I'm using. I get errors of the type >>> >>> ('rop-1.0.2/source/vprofile/G32965.GTEX-XAJ8-0726-SM-47JY5.3.unmapped_after_rRNA_virus_blastFormat6.csv', >>> '/apps/software/ROP/1.0.2-Python-2.7.11-foss-2015b/source/vprofile/G32965.GTEX-XAJ8-0726-SM-47JY5.3.unmapped_after_rRNA_virus_blastFormat6.csv', >>> "[Errno 2] No such file or directory: >>> 'rop-1.0.2/source/vprofile/G32965.GTEX-XAJ8-0726-SM-47JY5.3.unmapped_after_rRNA_virus_blastFormat6.csv'"), >>> >>> See attached .log file for full log. >>> >>> Our install buildpath is in /apps/.tmp/, and there I can find the file >>> that should be copied, i.e this is the path to the existing file >>> /apps/.tmp/easybuild/builds/ROP/1.0.2/dummy-dummy-Python-2.7.11-foss-2015b/rop-1.0.2/source/vprofile/G32965.GTEX-XAJ8-0726-SM-47JY5.3.unmapped_after_rRNA_virus_blastFormat6.csv, >>> and the path it should copy to also exists: >>> >>> ls >>> /apps/software/ROP/1.0.2-Python-2.7.11-foss-2015b/source/vprofile/ >>> extractViralReads2.py extractViralReads.py >>> G32965.GTEX-XAJ8-0726-SM-47JY5.3.unmapped_after_rRNA_virus_blastFormat6_filtered.csv >>> >>> And it did copy some of the files to that folder. >>> >>> Any idea what I am doing wrong? >>> >>> Thanks, >>> Niek >>> >> >> >
