diff --git a/docs/index.rst b/docs/index.rst index 30eeb82a1..651f99458 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -4,7 +4,7 @@ contain the root `toctree` directive. The Activity-by-Contact (ABC) Model for predicting enhancer-gene regulatory interactions -======================================================== +======================================================================================== The Activity-by-Contact (ABC) model predicts which enhancers regulate which genes in a given cell type, based on a combination of input datasets representing enhancer activity and 3D enhancer-promoter contact frequency [1]. @@ -47,6 +47,7 @@ v0.2 (version for [1]) usage/getting_started usage/methods usage/scATAC + usage/troubleshooting .. toctree:: diff --git a/docs/usage/troubleshooting.rst b/docs/usage/troubleshooting.rst new file mode 100644 index 000000000..6cdd211cd --- /dev/null +++ b/docs/usage/troubleshooting.rst @@ -0,0 +1,12 @@ +Troubleshooting +=============== + +Conda Env Building Issues +----------------------------- +Building the conda environment can take a lot of resources, especially if you're not using `mamba`. Make sure the process isn't being killed +(e.g because it's taking up too many resources in a shared environment). If it is, make sure you try building the environment with more resources. + +If you're on MacOSX, make sure to remove some of the requirements in abcenv.yml. Those requirements to delete are flagged in the file. + +If there are incompatibility issues, try building off the 'release.yml' conda environment. + diff --git a/workflow/envs/release.yml b/workflow/envs/release.yml index f99d6fe0e..959a66c22 100644 --- a/workflow/envs/release.yml +++ b/workflow/envs/release.yml @@ -80,6 +80,7 @@ dependencies: - dropbox=11.36.2=pyhd8ed1ab_0 - eido=0.2.2=pyhd8ed1ab_0 - exceptiongroup=1.2.0=pyhd8ed1ab_2 + - execnet=2.0.2=pyhd8ed1ab_0 - expat=2.5.0=hcb278e6_1 - filechunkio=1.8=py_2 - fmt=10.2.1=h00ab1b0_0 @@ -293,6 +294,7 @@ dependencies: - pysftp=0.2.9=py_1 - pysocks=1.7.1=pyha2e5f31_6 - pytest=8.0.2=pyhd8ed1ab_0 + - pytest-xdist=3.5.0=pyhd8ed1ab_0 - python=3.10.13=hd12c33a_1_cpython - python-dateutil=2.9.0=pyhd8ed1ab_0 - python-fastjsonschema=2.19.1=pyhd8ed1ab_0