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authorThomas White <htcc01@max-display001.desy.de>2020-01-23 21:16:24 +0100
committerThomas White <taw@physics.org>2020-01-23 21:19:58 +0100
commit2a28723b8158b1e310a6a56df04323828b83b38e (patch)
tree7a3745bcbb24b7ca7a923555cc748896f307ad9b
parentb68013b2d3ad4bdc749ddb2e0fc7cbb7610b3e95 (diff)
Fix conda pathsHEADmaster
-rw-r--r--files/calc-foms.sh4
-rw-r--r--files/run-cell.sh4
-rw-r--r--files/run-nocell.sh4
-rw-r--r--files/run-peaks.sh4
4 files changed, 8 insertions, 8 deletions
diff --git a/files/calc-foms.sh b/files/calc-foms.sh
index ef2e28a..1e8b4fa 100644
--- a/files/calc-foms.sh
+++ b/files/calc-foms.sh
@@ -1,7 +1,7 @@
#!/bin/sh
-source /gpfs/cfel/cxi/common/public/cfelsoft-rh7-public/conda-setup.sh
-conda activate cfel_crystallography
+module load maxwell miniconda3
+conda activate /gpfs/cfel/cxi/scratch/user/twhite/conda/envs/crystfel_dev
set -x
diff --git a/files/run-cell.sh b/files/run-cell.sh
index d4e48fc..3aac146 100644
--- a/files/run-cell.sh
+++ b/files/run-cell.sh
@@ -12,7 +12,7 @@
#module load crystallography/latest
#export PATH=/install/bin:$PATH
-source /gpfs/cfel/cxi/common/public/cfelsoft-rh7-public/conda-setup.sh
-conda activate cfel_crystallography
+module load maxwell miniconda3
+conda activate /gpfs/cfel/cxi/scratch/user/twhite/conda/envs/crystfel_dev
indexamajig -i files.lst -o cell.stream -j `nproc` -g 5HT2B-Liu-2013.geom --peaks=peakfinder8 --threshold=800 --min-pix-count=1 --min-snr=3 -p 5HT2B.cell --indexing=xgandalf,mosflm
diff --git a/files/run-nocell.sh b/files/run-nocell.sh
index 7b778e1..bb0bb72 100644
--- a/files/run-nocell.sh
+++ b/files/run-nocell.sh
@@ -12,7 +12,7 @@
#module load crystallography/latest
#export PATH=/install/bin:$PATH
-source /gpfs/cfel/cxi/common/public/cfelsoft-rh7-public/conda-setup.sh
-conda activate cfel_crystallography
+module load maxwell miniconda3
+conda activate /gpfs/cfel/cxi/scratch/user/twhite/conda/envs/crystfel_dev
indexamajig -i files.lst -o nocell.stream -j `nproc` -g 5HT2B-Liu-2013.geom --peaks=peakfinder8 --threshold=800 --min-pix-count=1 --min-snr=3 --indexing=mosflm
diff --git a/files/run-peaks.sh b/files/run-peaks.sh
index 41d5248..dc8fe31 100644
--- a/files/run-peaks.sh
+++ b/files/run-peaks.sh
@@ -12,7 +12,7 @@
#module load crystallography/latest
#export PATH=/install/bin:$PATH
-source /gpfs/cfel/cxi/common/public/cfelsoft-rh7-public/conda-setup.sh
-conda activate cfel_crystallography
+module load maxwell miniconda3
+conda activate /gpfs/cfel/cxi/scratch/user/twhite/conda/envs/crystfel_dev
indexamajig -i files.lst -o peaks.stream -j `nproc` -g 5HT2B-Liu-2013.geom --peaks=peakfinder8 --threshold=800 --min-pix-count=1 --min-snr=3 --indexing=none