From 9e154601bb7224c10916f865b33d170b9e3b6ffb Mon Sep 17 00:00:00 2001
From: Niko Papadopoulos <nikolaos.papadopoulos@embl.de>
Date: Tue, 2 Aug 2022 06:38:47 +0000
Subject: [PATCH] update scripts to new paths, new conda env name
---
scripts/align.sh | 4 ++--
scripts/databases.sh | 2 +-
scripts/predict_structures.sh | 2 +-
scripts/submit_colab.sh | 2 +-
4 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/scripts/align.sh b/scripts/align.sh
index 71111ed..c1e63c5 100755
--- a/scripts/align.sh
+++ b/scripts/align.sh
@@ -11,7 +11,7 @@ module load GCC
module load bzip2
module load CUDA
source ~/.bash_profile
-conda activate /g/arendt/npapadop/repos/condas/maf
+conda activate /g/arendt/npapadop/repos/condas/CoFFE
MMSEQS="/g/arendt/npapadop/repos/MMseqs2/build/bin/mmseqs"
QUERY="/g/arendt/data/spongilla_singlecell_dataset/spongilla_lacustris_Trinity.fasta.transdecoder_70AA_mediumheader.fasta"
@@ -20,4 +20,4 @@ BASE="/scratch/npapadop/"
cd "${BASE}"
colabfold_search "${QUERY}" database/ ./ --mmseqs "${MMSEQS}" --threads 32
-module unload
\ No newline at end of file
+module unload
diff --git a/scripts/databases.sh b/scripts/databases.sh
index f952198..499d9c6 100755
--- a/scripts/databases.sh
+++ b/scripts/databases.sh
@@ -69,4 +69,4 @@ if [ ! -f COLABDB_READY ]; then
fi
module unload aria2
-module unload bzip2
\ No newline at end of file
+module unload bzip2
diff --git a/scripts/predict_structures.sh b/scripts/predict_structures.sh
index 7fb769a..dd26834 100755
--- a/scripts/predict_structures.sh
+++ b/scripts/predict_structures.sh
@@ -20,7 +20,7 @@ shift
shift
unset CONDA_SHLVL
eval "$(conda shell.bash hook)"
-conda activate /g/arendt/npapadop/repos/condas/milot
+conda activate /g/arendt/npapadop/repos/condas/CoFFE
export TF_FORCE_UNIFIED_MEMORY=1
mkdir -p ${OUTPUT}
colabfold_batch "$INPUT" "$OUTPUT" --stop-at-score 85
diff --git a/scripts/submit_colab.sh b/scripts/submit_colab.sh
index 0b7be96..6c70c55 100755
--- a/scripts/submit_colab.sh
+++ b/scripts/submit_colab.sh
@@ -1,5 +1,5 @@
#!/bin/bash -ex
for i in $(seq 1 32); do
- sbatch /g/arendt/npapadop/repos/spongfold/milot.sh /scratch/npapadop/msas/batch"$i" /scratch/npapadop/res_batch"$i"
+ sbatch /g/arendt/npapadop/repos/spongfold/scripts/predict_structures.sh /scratch/npapadop/msas/batch"$i" /scratch/npapadop/res_batch"$i"
done
--
GitLab