Fix/builds (#665)

* fix: jq from source needs dependencies * modify centos repos if available * command escaping in shell * fix: line endings * more fixes for shell and fedora * fix accidental change

Author: satra

neurodocker/cli/tests/sample-template-jq.yaml

@@ -17,10 +17,12 @@ binaries:
  ND_BAZ: '1234'
  ND_FOO: BAR
  instructions: |
- export DUMMY="dummy"
+ echo "Installing from binaries"
  {%- if self.pkg_manager == "yum" %}
- sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
- sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-*
+ if ls /etc/yum.repos.d/CentOS-* >/dev/null 2>&1; then
+ sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
+ sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-*;
+ fi
  {%- endif %}
  {{ self.install_dependencies() }}
  curl -fsSL --output /usr/local/bin/jq {{ self.urls[self.version]}}
@@ -53,10 +55,12 @@ source:
  ND_BAZ: '1234'
  ND_FOO: BAR
  instructions: |
- export DUMMY="dummy"
+ echo "Building from source"
  {%- if self.pkg_manager == "yum" %}
- sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
- sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-*
+ if ls /etc/yum.repos.d/CentOS-* >/dev/null 2>&1; then
+ sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
+ sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-*;
+ fi
  {%- endif %}
  {{ self.install_dependencies() }}
  mkdir jq

neurodocker/templates/_default.yaml

@@ -19,7 +19,6 @@ source:
  yum:
  - bzip2
  - ca-certificates
- - epel-release
  - unzip
  - glibc-langpack-en
  - glibc-locale-source