Merge pull request #32916 from jbedo/singularity-2.4

singularity: 2.2 -> 2.4

pkgs/applications/virtualization/singularity/default.nix

@@ -1,20 +1,52 @@
 { stdenv
 , fetchFromGitHub
-, autoreconfHook }:
+, autoreconfHook
+, gnutar
+, which
+, gnugrep
+, coreutils
+, python
+, e2fsprogs
+, makeWrapper
+, squashfsTools
+, gzip
+, gnused
+, curl
+, utillinux
+ }:
 
 stdenv.mkDerivation rec {
   name = "singularity-${version}";
-  version = "2.2";
+  version = "2.4";
+
+  enableParallelBuilding = true;
+
+  patches = [ ./env.patch ];
+
+  preConfigure = ''
+    sed -i 's/-static//g' src/Makefile.am
+    patchShebangs .
+  '';
+
+  fixupPhase = ''
+    patchShebangs $out
+    for f in $out/libexec/singularity/helpers/help.sh $out/libexec/singularity/cli/*.exec $out/libexec/singularity/bootstrap-scripts/*.sh ; do
+      chmod a+x $f
+      sed -i 's| /sbin/| |g' $f
+      sed -i 's| /bin/bash| ${stdenv.shell}|g' $f
+      wrapProgram $f --prefix PATH : ${stdenv.lib.makeBinPath buildInputs}
+    done
+  '';
 
   src = fetchFromGitHub {
     owner = "singularityware";
     repo = "singularity";
     rev = version;
-    sha256 = "19g43gfdy5s8y4252474cp39d6ypn5dd37wp0s21fgd13vqy26px";
+    sha256 = "1hi1ag1lb2x4djbz4x34wix83ymx0g9mzn2md6yrpiflc1d85rjz";
   };
 
-  nativeBuildInputs = [ autoreconfHook ];
-  buildInputs = [ ];
+  nativeBuildInputs = [ autoreconfHook makeWrapper ];
+  buildInputs = [ coreutils gnugrep python e2fsprogs which gnutar squashfsTools gzip gnused curl utillinux ];
 
   meta = with stdenv.lib; {
     homepage = http://singularity.lbl.gov/;

pkgs/applications/virtualization/singularity/env.patch

@@ -0,0 +1,21 @@
+diff --git a/libexec/functions b/libexec/functions
+index bc68107..6c2211c 100644
+--- a/libexec/functions
++++ b/libexec/functions
+@@ -29,16 +29,6 @@ if [ -z "${SINGULARITY_MESSAGELEVEL:-}" ]; then
+     SINGULARITY_MESSAGELEVEL=5
+ fi
+ 
+-if [ -z "${USER:-}" ]; then
+-    USER=`id -un`
+-    export USER
+-fi
+-if [ -z "${HOME:-}" ]; then
+-    HOME=`getent passwd "$USER" | cut -d : -f 6`
+-    export HOME
+-fi
+-
+-
+ message() {
+     LEVEL="${1:-}"
+     MESSAGE="${2:-}"

pkgs/build-support/singularity-tools/default.nix

@@ -61,6 +61,7 @@ rec {
             mkfs -t ext3 -b 4096 /dev/${vmTools.hd}
             mount /dev/${vmTools.hd} disk
             cd disk
+            mkdir proc sys dev
 
             # Run root script
             ${stdenv.lib.optionalString (runAsRoot != null) ''
@@ -92,8 +93,10 @@ rec {
             cd disk
 
             export PATH=$PATH:${e2fsprogs}/bin/
-            singularity create -s $((1 + size * 4 / 1024 + ${toString extraSpace})) $out
-            tar -c . | singularity import $out
+            echo creating
+            singularity image.create -s $((1 + size * 4 / 1024 + ${toString extraSpace})) $out
+            echo importing
+            tar -c . | singularity image.import $out
           '');
 
     in result;