Problem installing phyluce using miniconda

[SilAdSe]

Hello, my name is Silvia. I am attempting to install the phyluce package for linux in my user in a cluster using miniconda and following the instructions given in the phyluce github release page but I am getting the following error:

Solving environment: failed

ResolvePackageNotFound:

• nbformat==5.1.2=pyhd8ed1ab_1

It had already installed it a few months ago and successfully used it until today. The last process I run was pphyluce_assembly_assemblo_spades, but I had been getting some errors indicating that I needed to allocate more RAM. I had been doing different trials increasing the --memory flag each time and when I saw it wasn't generating the contigs output I killed it and deleted the outputs to make a new trial allocating more memory. The last I tried was --memory 100, it failed, I killed it and it took it a lot of time to delate the outputs in the spades_assembly folder. After that, the next trial didn't work and it gave me the following error:

Traceback (most recent call last): File "/users-d3/sadrian/miniconda3/envs/phyluce-1.7.1/bin/phyluce_assembly_assemblo_spades", line 19, in from phyluce.helpers import FullPaths, is_dir, is_file File "/users-d3/sadrian/miniconda3/envs/phyluce-1.7.1/lib/python3.6/site-packages/phyluce/init.py", line 21, in cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT File "/users-d3/sadrian/miniconda3/envs/phyluce-1.7.1/lib/python3.6/subprocess.py", line 729, in init restore_signals, start_new_session) File "/users-d3/sadrian/miniconda3/envs/phyluce-1.7.1/lib/python3.6/subprocess.py", line 1364, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) OSError: [Errno 116] Stale file handle: 'git'

I tried a couple of times but it was always the same. I thought maybe some file in the phyluce environment had been corrupted so I decided to try to delete and install it again. But now I am not being able to install the package, have no clue of what is happening and need some support with that. Thank you very much in advance.

[brantfaircloth]

Hello,

I am working on an update to fix that issue you are having with reinstalling, but I'm not quite ready to post the update. In the meantime, you can:

wget https://raw.githubusercontent.com/faircloth-lab/phyluce/main/distrib/phyluce-1.7.2-py36-Linux-conda.yml

and then install phyluce using that yml file versus the one for 1.7.1. This should fix the first issue. I am not sure of the cause of the second issue - see if re-installing fixes it, first.

[brantfaircloth]

This has now been updated in the 1.7.2 release..

[SilAdSe]

Thank you, I successfully installed the new version of phyluce. I managed to run phyluce_assembly_assemblo_spades in another node in the cluster, so it seems to be a cluster problem. Thank you again, have a nice weekend.