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
