From 27619cd8ced6b7d070e208acc27458e2f4ada269 Mon Sep 17 00:00:00 2001
From: jsmentch <jsmentch@gmail.com>
Date: Fri, 27 Mar 2020 13:04:45 -0400
Subject: [PATCH] making 2 files, one for debian, one for centos for bug fix

---
 Singularity.centos                | 146 ++++++++++++++++++++++++++++++
 Singularity => Singularity.debian |   0
 2 files changed, 146 insertions(+)
 create mode 100644 Singularity.centos
 rename Singularity => Singularity.debian (100%)

diff --git a/Singularity.centos b/Singularity.centos
new file mode 100644
index 0000000..0556db6
--- /dev/null
+++ b/Singularity.centos
@@ -0,0 +1,146 @@
+# Your version: 0.6.0 Latest version: 0.6.0
+# Generated by Neurodocker version 0.6.0
+# Timestamp: 2020-03-27 17:03:07 UTC
+# 
+# Thank you for using Neurodocker. If you discover any issues
+# or ways to improve this software, please submit an issue or
+# pull request on our GitHub repository:
+# 
+#     https://github.com/kaczmarj/neurodocker
+
+Bootstrap: docker
+From: centos
+
+%post
+export ND_ENTRYPOINT="/neurodocker/startup.sh"
+yum install -y -q \
+    bzip2 \
+    ca-certificates \
+    curl \
+    localedef \
+    unzip
+yum clean packages
+rm -rf /var/cache/yum/*
+localedef -i en_US -f UTF-8 en_US.UTF-8
+chmod 777 /opt && chmod a+s /opt
+mkdir -p /neurodocker
+if [ ! -f "$ND_ENTRYPOINT" ]; then
+  echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT"
+  echo 'set -e' >> "$ND_ENTRYPOINT"
+  echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT"
+  echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT";
+fi
+chmod -R 777 /neurodocker && chmod a+s /neurodocker
+
+export PATH="/opt/miniconda-latest/bin:$PATH"
+echo "Downloading Miniconda installer ..."
+conda_installer="/tmp/miniconda.sh"
+curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+bash "$conda_installer" -b -p /opt/miniconda-latest
+rm -f "$conda_installer"
+conda update -yq -nbase conda
+conda config --system --prepend channels conda-forge
+conda config --system --set auto_update_conda false
+conda config --system --set show_channel_urls true
+sync && conda clean --all && sync
+conda create -y -q --name neuro
+conda install -y -q --name neuro \
+    "numpy" \
+    "pandas" \
+    "scipy" \
+    "scikit-learn" \
+    "matplotlib" \
+    "seaborn" \
+    "networkx" \
+    "ipython" \
+    "joblib" \
+    "nibabel" \
+    "datalad" \
+    "jupyter"
+sync && conda clean --all && sync
+bash -c "source activate neuro
+  pip install --no-cache-dir  \
+      "nibabel" \
+      "ply" \
+      "neurosynth" \
+      "nilearn" \
+      "pliers" \
+      "kmapper" \
+      "dyneusr""
+rm -rf ~/.cache/pip/*
+sync
+
+
+yum install -y None \
+    emacs
+yum clean packages
+rm -rf /var/cache/yum/*
+
+test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
+su - neuro
+
+echo '{
+\n  "pkg_manager": "yum",
+\n  "instructions": [
+\n    [
+\n      "base",
+\n      "centos"
+\n    ],
+\n    [
+\n      "_header",
+\n      {
+\n        "version": "generic",
+\n        "method": "custom"
+\n      }
+\n    ],
+\n    [
+\n      "miniconda",
+\n      {
+\n        "create_env": "neuro",
+\n        "conda_install": [
+\n          "numpy",
+\n          "pandas",
+\n          "scipy",
+\n          "scikit-learn",
+\n          "matplotlib",
+\n          "seaborn",
+\n          "networkx",
+\n          "ipython",
+\n          "joblib",
+\n          "nibabel",
+\n          "datalad",
+\n          "jupyter"
+\n        ],
+\n        "pip_install": [
+\n          "nibabel",
+\n          "ply",
+\n          "neurosynth",
+\n          "nilearn",
+\n          "pliers",
+\n          "kmapper",
+\n          "dyneusr"
+\n        ]
+\n      }
+\n    ],
+\n    [
+\n      "install",
+\n      [
+\n        "emacs"
+\n      ]
+\n    ],
+\n    [
+\n      "user",
+\n      "neuro"
+\n    ]
+\n  ]
+\n}' > /neurodocker/neurodocker_specs.json
+
+%environment
+export LANG="en_US.UTF-8"
+export LC_ALL="en_US.UTF-8"
+export ND_ENTRYPOINT="/neurodocker/startup.sh"
+export CONDA_DIR="/opt/miniconda-latest"
+export PATH="/opt/miniconda-latest/bin:$PATH"
+
+%runscript
+/neurodocker/startup.sh "$@"
diff --git a/Singularity b/Singularity.debian
similarity index 100%
rename from Singularity
rename to Singularity.debian