Open carlo-deintinis opened 3 years ago
Hi Carlo,
I don't have any direct advice for getting it to work in Singularity.
It looks from that that it can't find your config file. Can you use the -c
option to point to the tracer/docker_helper_files/docker_tracer.conf
file?
Also, see this issue for something else that was encountered previously with Singularity: https://github.com/Teichlab/tracer/issues/87.
Let me know if that helps,
Mike
Thank you for your answer!
running singularity exec -H $PWD $PWD/tracer.simg tracer test -c tracer-master/docker_helper_files/docker_tracer.conf
results in
Traceback (most recent call last):
File "/usr/local/bin/tracer", line 11, in <module>
load_entry_point('tracer==0.5', 'console_scripts', 'tracer')()
File "/usr/local/lib/python3.7/dist-packages/tracer-0.5-py3.7.egg/tracerlib/launcher.py", line 43, in launch
Task().run()
File "/usr/local/lib/python3.7/dist-packages/tracer-0.5-py3.7.egg/tracerlib/tasks.py", line 1224, in run
loci=['A', 'B'], max_junc_len=50).run()
File "/usr/local/lib/python3.7/dist-packages/tracer-0.5-py3.7.egg/tracerlib/tasks.py", line 358, in run
io.makeOutputDir(self.output_dir)
File "/usr/local/lib/python3.7/dist-packages/tracer-0.5-py3.7.egg/tracerlib/io.py", line 26, in makeOutputDir
os.makedirs(output_dir_path)
File "/usr/lib/python3.7/os.py", line 221, in makedirs
mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/tracer/test_data/results/cell1'
The first idea that comes to mind is that docker containers run as root by default, whereas singularity ones do not follow that behaviour. A whoami
inside the docker container results in root, whereas in sinology it results in my username.
Hi Carlo,
I think you might be right about the permissions. I found this: https://github.com/hpcng/singularity/issues/1132#issuecomment-407104957 which suggests using a Singularity def file to chmod
the directories you need. Can you do that?
Sorry, I don't have any experience with Singularity so I can't be that much help.
Please let me know if you manage to make this work.
Cheers,
Mike
On 9 Dec 2020, at 11:54, carlo-deintinis notifications@github.com wrote:
Thank you for your answer!
running singularity exec -H $PWD $PWD/tracer.simg tracer test -c tracer-master/docker_helper_files/docker_tracer.conf results in
Traceback (most recent call last): File "/usr/local/bin/tracer", line 11, in
load_entry_point('tracer==0.5', 'console_scripts', 'tracer')() File "/usr/local/lib/python3.7/dist-packages/tracer-0.5-py3.7.egg/tracerlib/launcher.py", line 43, in launch Task().run() File "/usr/local/lib/python3.7/dist-packages/tracer-0.5-py3.7.egg/tracerlib/tasks.py", line 1224, in run loci=['A', 'B'], max_junc_len=50).run() File "/usr/local/lib/python3.7/dist-packages/tracer-0.5-py3.7.egg/tracerlib/tasks.py", line 358, in run io.makeOutputDir(self.output_dir) File "/usr/local/lib/python3.7/dist-packages/tracer-0.5-py3.7.egg/tracerlib/io.py", line 26, in makeOutputDir os.makedirs(output_dir_path) File "/usr/lib/python3.7/os.py", line 221, in makedirs mkdir(name, mode) PermissionError: [Errno 13] Permission denied: '/tracer/test_data/results/cell1' The first idea that comes to mind is that docker containers run as root by default, whereas singularity ones do not follow that behaviour. A whoami inside the docker container results in root, whereas in sinology it results in my username. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Teichlab/tracer/issues/109#issuecomment-741723841, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIXBBRPXEFZAHHEPLJZIILST5QOXANCNFSM4UTJBPOQ.
In the end, I did not pursue the road of Singularity any further due to many errors and lack of permissions on the cluster on which I was trying to run the analysis.
I was able to create a conda environment with the smallest number of conflicts I could manage between dependencies and run Tracer in there (the assemble and summarise steps work, skipping the plots). I got identical analysis results from the docker image.
However, managing all program versions and python dependencies was a mess (some are still not the same as the ones inside the docker image). Do you by any chance plan to release Tracer as a conda package?
Thank you for developing tracer!
I am currently trying to run the tracer docker container using singularity without success.
If for example I run
docker run teichlab/tracer test
I get the expected results.However, trying to do the same in singularity with the command
singularity run tracer.simg test
(orsingularity exec tracer.simg tracer test
) results inRunning the image without arguments seems to work fine:
singularity run tracer.simg
results inAny suggestions? Thanks in advance for the help.