fix: jq from source needs dependencies (#663)

* fix: jq from source needs dependencies * modify centos repos if available

Author: satra

neurodocker/templates/_default.yaml

@@ -30,8 +30,11 @@ source:
  instructions: |
  export ND_ENTRYPOINT="{{ self.env['ND_ENTRYPOINT'] }}"
  {%- 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
+ # Disable mirrorlist and switch to vault.centos.org
+ 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() }}
  {%- if self.pkg_manager == "apt" %}

neurodocker/templates/jq.yaml

@@ -43,6 +43,7 @@ source:
  - libtool
  - make
  instructions: |
+ {{ self.install_dependencies() }}
  mkdir jq
  cd jq
  curl -fsSL https://github.com/jqlang/jq/releases/download/jq-{{self.version}}/jq-{{self.version}}.tar.gz \