From e85b13d0540457b9833b2a29a151e563526077ba Mon Sep 17 00:00:00 2001
From: Felix Perez <felix.perez@utsouthwestern.edu>
Date: Mon, 4 Mar 2024 15:57:01 -0600
Subject: [PATCH] Build first draft of the fix for the module error
encountered.
---
astrocyte_pkg.yml | 4 ++--
workflow/configs/biohpc.config | 3 ++-
workflow/main.nf | 5 +++--
3 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 0f884de..3413971 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -81,8 +81,8 @@ workflow_modules:
# Singularity supports different registries, please specify the protocol to use.
# Such as, "docker://", "shub://", "library://", etc. We encourage you to use the GitLab
# container registry of BioHPC to save and manage your container images.
-workflow_containers:
- - docker://git.biohpc.swmed.edu:5050/s219741/astrocyte-atac-source/atac:0.0.1
+#workflow_containers:
+# - docker://git.biohpc.swmed.edu:5050/s219741/astrocyte-atac-source/atac:0.0.1
# A list of parameters used by the workflow, defining how to present them,
# options etc in the web interface. For each parameter:
diff --git a/workflow/configs/biohpc.config b/workflow/configs/biohpc.config
index 9ff1e4b..a83de14 100755
--- a/workflow/configs/biohpc.config
+++ b/workflow/configs/biohpc.config
@@ -1,3 +1,4 @@
+/*
singularity {
enabled = true
runOptions = ''
@@ -13,7 +14,7 @@ singularity {
cacheDir = "$baseDir/images/singularity" // Singularity images specified in `workflow_containers` of astrocyte_pkg.yml will be saved to
// this folder automatically, before running the workflow. The images will be renamed as
// "NAME-TAG.img", e.g. ubuntu-latest.img, centos-centos8.img, r-4.1.1.img, etc.
-}
+}*/
process {
executor = 'slurm'
diff --git a/workflow/main.nf b/workflow/main.nf
index 682a70d..f2894ee 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -29,8 +29,9 @@ process runSource {
shell:
'''
- module load python/3.8.x-anaconda
- module load openjdk/18
+ export PATH="/cm/shared/apps/openjdk/18/jdk-18/bin:/cm/shared/apps/python/3.8.x-anaconda/condabin:/cm/shared/apps/python/3.8.x-anaconda/bin:$PATH"
+ python --version > python_version.txt
+ java -version 2> java_version_before.txt
# Enable the use of bash-specific conda commands in this shell.
eval "$(conda shell.bash hook)"
--
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