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