f972863712
- add version 6.0.5 - add patch to allow fsl to use newer gcc versions - add patch to allow fsl to use newer cuda versions - remove constraints on gcc and cuda versions - add filters to prevent using system headers and libraries - clean up the installed tree
40 lines
2.9 KiB
Diff
40 lines
2.9 KiB
Diff
--- a/etc/fslconf/fslpython_install.sh 2020-07-25 09:20:04.000000000 -0500
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+++ b/etc/fslconf/fslpython_install.sh 2020-11-09 20:12:59.458736979 -0600
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@@ -204,19 +204,19 @@
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# - https://github.com/conda/conda/issues/8804
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# Try to make downloads more resilient
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-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_read_timeout_secs 240
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-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_connect_timeout_secs 20
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-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_max_retries 10
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-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_backoff_factor 5
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-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set safety_checks warn
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+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_read_timeout_secs 240
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+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_connect_timeout_secs 20
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+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_max_retries 10
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+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_backoff_factor 5
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+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set safety_checks warn
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# Channel priority:
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# - conda-forge (highest priority)
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# - defaults (gets automatically added on the first call)
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# - fsl (lowest priority)
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-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set channel_priority strict
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-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --add channels conda-forge
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-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --append channels https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel
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+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set channel_priority strict
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+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --add channels conda-forge
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+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --append channels https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel
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##############################
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@@ -229,7 +229,7 @@
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if [ ${quiet} -ne 1 ]; then
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echo "Stage 2"
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fi
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-FSLDIR=$fsl_dir "${miniconda_bin_dir}/conda" env create -v \
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+FSLDIR=$fsl_dir "${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda-env" create -v \
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-f "${script_dir}/fslpython_environment.yml" \
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2>> "${miniconda_install_log}" | \
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${script_dir}/progress.sh 133 ${quiet} 1>> "${miniconda_install_log}"
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