Closed paulmenzel closed 1 week ago
TMPDIR
is set to /scratch/local
in our environment, which does not seem to be available in the image. Setting TMPDIR
to /tmp
fixes the issue:
$ TMPDIR=/tmp apptainer run hictk_1.0.0.sif --help
INFO: gocryptfs not found, will not be able to use gocryptfs
Blazing fast tools to work with .hic and .cool files.
Usage: /usr/local/bin/hictk [OPTIONS] SUBCOMMAND
Options:
-h,--help Print this help message and exit
-V,--version Display program version information and exit
Subcommands:
balance Balance Hi-C matrices using ICE, SCALE, or VC.
convert Convert HiC matrices to a different format.
dump Dump data from .hic and Cooler files to stdout.
fix-mcool Fix corrupted .mcool files.
load Build .cool and .hic files from interactions in various text formats.
merge Merge multiple Cooler or .hic files into a single file.
rename-chromosomes, rename-chroms
Rename chromosomes found in a Cooler file.
validate Validate .hic and Cooler files.
zoomify Convert single-resolution Cooler and .hic files to multi-resolution by coarsening.
If you think, it’s a non-issue, please close.
Thanks for reporting this issue and sharing a reasonable workaround!
I think hictk
is doing the right thing by issuing an error when a temporary folder cannot be safely created, however I think the current error message is a bit cryptic for less experienced users.
I will keep this issue open as a reminder to output a better error message (something like failed to create a temporary folder: please make sure the environment variable TMPDIR is defined and pointing to an existing folder
).
Thank you for your quick response.
I will keep this issue open as a reminder to output a better error message (something like
failed to create a temporary folder: please make sure the environment variable TMPDIR is defined and pointing to an existing folder
).
I’d also add the value of the tried directory.
failed to create a temporary folder
/scratch/local
The fix for this issue should be part of the next release.
On my machines these are the new errors generated by hictk:
TMPDIR points to a non-existing folder:
TMPDIR="foobar" hictk --help
FAILURE! hictk encountered the following error: filesystem error: unable to safely determine the path where to store temporary files: temporary folder is set to "foobar" but folder does not exists: No such file or directory
TMPDIR is empty or undefined
TMPDIR="" hictk --help
FAILURE! hictk encountered the following error: filesystem error: unable to safely determine the path where to store temporary files: please make sure the environment variable TMPDIR is defined and pointing to an existing folder: No such file or directory