diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/fsl/fslpython_install_v6.patch')
| -rw-r--r-- | var/spack/repos/builtin/packages/fsl/fslpython_install_v6.patch | 39 |
1 files changed, 39 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/fsl/fslpython_install_v6.patch b/var/spack/repos/builtin/packages/fsl/fslpython_install_v6.patch new file mode 100644 index 0000000000..93eac4cb73 --- /dev/null +++ b/var/spack/repos/builtin/packages/fsl/fslpython_install_v6.patch @@ -0,0 +1,39 @@ +--- a/etc/fslconf/fslpython_install.sh 2020-07-25 09:20:04.000000000 -0500 ++++ b/etc/fslconf/fslpython_install.sh 2020-11-09 20:12:59.458736979 -0600 +@@ -204,19 +204,19 @@ + # - https://github.com/conda/conda/issues/8804 + + # Try to make downloads more resilient +-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_read_timeout_secs 240 +-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_connect_timeout_secs 20 +-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_max_retries 10 +-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_backoff_factor 5 +-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set safety_checks warn ++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_read_timeout_secs 240 ++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_connect_timeout_secs 20 ++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_max_retries 10 ++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_backoff_factor 5 ++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set safety_checks warn + + # Channel priority: + # - conda-forge (highest priority) + # - defaults (gets automatically added on the first call) + # - fsl (lowest priority) +-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set channel_priority strict +-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --add channels conda-forge +-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --append channels https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel ++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set channel_priority strict ++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --add channels conda-forge ++"${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 + + + ############################## +@@ -229,7 +229,7 @@ + if [ ${quiet} -ne 1 ]; then + echo "Stage 2" + fi +-FSLDIR=$fsl_dir "${miniconda_bin_dir}/conda" env create -v \ ++FSLDIR=$fsl_dir "${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda-env" create -v \ + -f "${script_dir}/fslpython_environment.yml" \ + 2>> "${miniconda_install_log}" | \ + ${script_dir}/progress.sh 133 ${quiet} 1>> "${miniconda_install_log}" |