failed in install

[lmanchon]

--Hi,

i try to install the package but it failed with:

python setup.py build install
running build
running build_py
copying lib/annot_utils/chr_name.py -> build/lib/annot_utils
copying lib/annot_utils/listExon.py -> build/lib/annot_utils
copying lib/annot_utils/boundary.py -> build/lib/annot_utils
copying lib/annot_utils/exon.py -> build/lib/annot_utils
copying lib/annot_utils/run.py -> build/lib/annot_utils
copying lib/annot_utils/utils.py -> build/lib/annot_utils
copying lib/annot_utils/listCoding.py -> build/lib/annot_utils
copying lib/annot_utils/init.py -> build/lib/annot_utils
copying lib/annot_utils/gene.py -> build/lib/annot_utils
copying lib/annot_utils/coding.py -> build/lib/annot_utils
error: can't copy 'lib/annot_utils/data/hg38': doesn't exist or not a regular file

it's strange because hg38 exist and is readable in the directory:

ls -1 lib/annot_utils/data/hg38

GCF_000001405.26.assembly.txt
refGene.txt.gz
wgEncodeGencodeBasicV24.txt.gz

do you have a clue please ?

thank you --

[Yuichi Shiraishi]

Hi,

Thank you very much for the interest in our package!
I cannot reproduce the error in my environment.
Could you tell me your environment?
Also, do you have the write access for the lib/annot_utils/data/hg38 directory?

My recommendations are

1. Try --user option:
   python setup.py build install --user

2. Try other environment (e.g., use of Amazon or Google cloud)

[lmanchon]

Yuichi Shiraishi <[e-mail]> a écrit :

Hi, Thank you very much for the interest in our package! I cannot reproduce the error in my environment. Could you tell me your environment?

Python 2.7.2 (default, Mar 21 2012, 15:22:02) [GCC 4.4.6 20110731 (Red Hat 4.4.6-3)] on linux2

Also, do you have the write access for the lib/annot_utils/data/hg38 directory?

yes of course: ls -al lib/annot_utils/data/hg38 total 13897 drwxr-xr-x 2 127 May 24 16:05 . drwxr-xr-x 5 66 May 24 16:01 .. -rwxr-xr-x 1 54101 May 24 16:01 GCF_000001405.26.assembly.txt -rwxr-xr-x 1 5974540 May 21 16:02 refGene.txt.gz -rwxr-xr-x 1 5130670 Jul 17 2016 wgEncodeGencodeBasicV24.txt.gz

My recommendations are 1. Try --user option: python setup.py build install --user

again same error: python setup.py build install --user running build running build_py copying lib/annot_utils/chr_name.py -> build/lib/annot_utils copying lib/annot_utils/listExon.py -> build/lib/annot_utils copying lib/annot_utils/boundary.py -> build/lib/annot_utils copying lib/annot_utils/exon.py -> build/lib/annot_utils copying lib/annot_utils/run.py -> build/lib/annot_utils copying lib/annot_utils/utils.py -> build/lib/annot_utils copying lib/annot_utils/listCoding.py -> build/lib/annot_utils copying lib/annot_utils/__init__.py -> build/lib/annot_utils copying lib/annot_utils/gene.py -> build/lib/annot_utils copying lib/annot_utils/coding.py -> build/lib/annot_utils error: can't copy 'lib/annot_utils/data/hg38': doesn't exist or not a regular file

…

2. Try other environment (e.g., use of Amazon or Google cloud) -- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: #1 (comment)