Using '~' (A.K.A. tilde) in input directive does not seem to work? - tilde

Question

This is the first time I've tried to use a "~" in my input.
It works when I convert the "~" to an absolute path.
Proof they are the same file:
(CentOS5-Compatible) [tboyarski#login2 6-bamMetrics]$ ls ~/share/references/rRNA.ensg72.hg19.interval_list
-rw-rw-r-- 1 fcchan users 24K Dec 12 2013 /home/tboyarski/share/references/rRNA.ensg72.hg19.interval_list
(CentOS5-Compatible) [tboyarski#login2 6-bamMetrics]$ ls /genesis/extscratch/clc/references/rRNA.ensg72.hg19.interval_list
-rw-rw-r-- 1 fcchan users 24K Dec 12 2013 /genesis/extscratch/clc/references/rRNA.ensg72.hg19.interval_list
(CentOS5-Compatible) [tboyarski#login2 6-bamMetrics]$ ls /home/tboyarski/share/references/rRNA.ensg72.hg19.interval_list
-rw-rw-r-- 1 fcchan users 24K Dec 12 2013 /home/tboyarski/share/references/rRNA.ensg72.hg19.interval_list
Doesn't work:
rule intervalList:
input:
"~/share/references/rRNA.ensg72.hg19.interval_list"
Works:
rule intervalList:
input:
"/home/tboyarski/share/references/rRNA.ensg72.hg19.interval_list"
I've only tried using it in the input directive at this time. I might spend a moment to see if it works as an output directive (not something I need, just curious).
Thoughts?
EDIT
#alvits Was able to point out that ~ is converted by the shell to ${HOME} before it gets evaluated. It would seem that when providing ~ to snakemake, this conversion does not occurr. Easy alternative is to just always use ${HOME}, which works both on MacOSX and Linux :).
I was able to use the following successfully:
rule intervalList:
input:
"${HOME}/share/references/rRNA.ensg72.hg19.interval_list"
Second EDIT
User pointed out what I thought was a solution was in fact not.
Solution is to not use either "~" or "${HOME}" in the input directive.

Answer 1

You may try wrapping the path in os.path.expanduser (available after import os in your snakefile):
On Unix and Windows, return the argument with an initial component of ~ or ~user replaced by that user‘s home directory.
(Quoted from the documentation: https://docs.python.org/3/library/os.path.html#os.path.expanduser)

Answer 2

I'm going to close this question.
I ended up going with #alvits suggestion.
I chose it because that is what tilde represents, so it makes sense to provide it in an non-referenced form.
expanduser wrapping, although a possibility, is overkill for what is required.
Thank you everyone for your help!
2017/06/09 - EDIT: Don't use "~" or "${HOME}" in Snakemake inputs.
After seeing the comment by Johannes Köster, I double checked what I had done, and I was unable to reproduce it.
I'm sorry for the confusion. Thank you so much for catching this error J.K.
I'm not sure what I had setup prior. I ended up changing the way the file is being used, even with git, I cannot reproduce it.