From 2a28723b8158b1e310a6a56df04323828b83b38e Mon Sep 17 00:00:00 2001 From: Thomas White Date: Thu, 23 Jan 2020 21:16:24 +0100 Subject: Fix conda paths --- files/calc-foms.sh | 4 ++-- files/run-cell.sh | 4 ++-- files/run-nocell.sh | 4 ++-- files/run-peaks.sh | 4 ++-- 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 -- cgit v1.2.3