From 086d5998dd575c30f5ee5638c5b853fe67f85eac Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 18 Jun 2019 12:05:42 +1000
Subject: [PATCH] singularity: 3.0.1 -> 3.2.1

---
 .../virtualization/singularity/default.nix    |  13 +-
 .../virtualization/singularity/deps.nix       | 670 +-----------------
 2 files changed, 5 insertions(+), 678 deletions(-)

diff --git a/pkgs/applications/virtualization/singularity/default.nix b/pkgs/applications/virtualization/singularity/default.nix
index 12057c221e8f..8ec9ec6c8b49 100644
--- a/pkgs/applications/virtualization/singularity/default.nix
+++ b/pkgs/applications/virtualization/singularity/default.nix
@@ -15,13 +15,13 @@ with lib;
 
 buildGoPackage rec {
   name = "singularity-${version}";
-  version = "3.0.1";
+  version = "3.2.1";
 
   src = fetchFromGitHub {
     owner = "sylabs";
     repo = "singularity";
     rev = "v${version}";
-    sha256 = "1wpsd0il2ipa2n5cnbj8dzs095jycdryq2rx62kikbq7ahzz4fsi";
+    sha256 = "14lhxwy21s7q081x7kbnvkjsbxgsg2f181qlzmlxcn6n7gfav3kj";
   };
 
   goPackagePath = "github.com/sylabs/singularity";
@@ -32,22 +32,16 @@ buildGoPackage rec {
   propagatedBuildInputs = [ coreutils squashfsTools ];
 
   postConfigure = ''
-    find . -name vendor -type d -print0 | xargs -0 rm -rf
-
     cd go/src/github.com/sylabs/singularity
 
     patchShebangs .
-    sed -i 's|defaultEnv := "/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin"|defaultEnv := "${stdenv.lib.makeBinPath propagatedBuildInputs}"|' src/cmd/singularity/cli/singularity.go
+    sed -i 's|defaultPath := "[^"]*"|defaultPath := "${stdenv.lib.makeBinPath propagatedBuildInputs}"|' cmd/internal/cli/actions.go
 
     ./mconfig -V ${version} -p $bin --localstatedir=/var
-    touch builddir/.dep-done
-    touch builddir/vendors-done
 
     # Don't install SUID binaries
     sed -i 's/-m 4755/-m 755/g' builddir/Makefile
 
-    # Point to base gopath
-    sed -i "s|^cni_vendor_GOPATH :=.*\$|cni_vendor_GOPATH := $NIX_BUILD_TOP/go/src/github.com/containernetworking/plugins/plugins|" builddir/Makefile
   '';
 
   buildPhase = ''
@@ -57,6 +51,7 @@ buildGoPackage rec {
   installPhase = ''
     make -C builddir install LOCALSTATEDIR=$bin/var
     chmod 755 $bin/libexec/singularity/bin/starter-suid
+    wrapProgram $bin/bin/singularity --prefix PATH : ${stdenv.lib.makeBinPath propagatedBuildInputs}
   '';
 
   postFixup = ''
diff --git a/pkgs/applications/virtualization/singularity/deps.nix b/pkgs/applications/virtualization/singularity/deps.nix
index 526202e75ae5..fe51488c7066 100644
--- a/pkgs/applications/virtualization/singularity/deps.nix
+++ b/pkgs/applications/virtualization/singularity/deps.nix
@@ -1,669 +1 @@
-# file generated from Gopkg.lock using dep2nix (https://github.com/nixcloud/dep2nix)
-[
-  {
-    goPackagePath  = "github.com/Microsoft/go-winio";
-    fetch = {
-      type = "git";
-      url = "https://github.com/Microsoft/go-winio";
-      rev =  "7da180ee92d8bd8bb8c37fc560e673e6557c392f";
-      sha256 = "19gjjhmzswhm11wzj38r5alxypmflmy0z42flhc3czhmmwv7b1av";
-    };
-  }
-  {
-    goPackagePath  = "github.com/alexflint/go-filemutex";
-    fetch = {
-      type = "git";
-      url = "https://github.com/alexflint/go-filemutex";
-      rev =  "d358565f3c3f5334209f1e80693e4f621650c489";
-      sha256 = "19fzbm0x8821awsmqj9ig49dxxkd72p1yfqbijmdwwszvw2r0ggz";
-    };
-  }
-  {
-    goPackagePath  = "github.com/beorn7/perks";
-    fetch = {
-      type = "git";
-      url = "https://github.com/beorn7/perks";
-      rev =  "3a771d992973f24aa725d07868b467d1ddfceafb";
-      sha256 = "1l2lns4f5jabp61201sh88zf3b0q793w4zdgp9nll7mmfcxxjif3";
-    };
-  }
-  {
-    goPackagePath  = "github.com/blang/semver";
-    fetch = {
-      type = "git";
-      url = "https://github.com/blang/semver";
-      rev =  "2ee87856327ba09384cabd113bc6b5d174e9ec0f";
-      sha256 = "13ws259bwcibkclbr82ilhk6zadm63kxklxhk12wayklj8ghhsmy";
-    };
-  }
-  {
-    goPackagePath  = "github.com/containerd/cgroups";
-    fetch = {
-      type = "git";
-      url = "https://github.com/containerd/cgroups";
-      rev =  "5017d4e9a9cf2d4381db99eacd9baf84b95bfb14";
-      sha256 = "02pvcmj91j3maa9j1v91m2z9kpa6p822h06r007b3pl7h0paiqnj";
-    };
-  }
-  {
-    goPackagePath  = "github.com/containerd/continuity";
-    fetch = {
-      type = "git";
-      url = "https://github.com/containerd/continuity";
-      rev =  "246e49050efdf45e8f17fbbcf1547ee376f9939e";
-      sha256 = "1zc1f0yixf32lprp5r77z2j9xq7fk0hijq8xzl08j4zrk0fcy8aq";
-    };
-  }
-  {
-    goPackagePath  = "github.com/containernetworking/cni";
-    fetch = {
-      type = "git";
-      url = "https://github.com/containernetworking/cni";
-      rev =  "a7885cb6f8ab03fba07852ded351e4f5e7a112bf";
-      sha256 = "00ajs2r5r2z3l0vqwxrcwhjfc9px12qbcv5vnvs2mdipvvls1y2y";
-    };
-  }
-  {
-    goPackagePath  = "github.com/containernetworking/plugins";
-    fetch = {
-      type = "git";
-      url = "https://github.com/containernetworking/plugins";
-      rev =  "2b8b1ac0af4568e928d96ccc5f47b075416eeabd";
-      sha256 = "1yl9m8pwjmqxj3hf0w9s6rykszhcww54z07yjgxzabmqf2dhchxv";
-    };
-  }
-  {
-    goPackagePath  = "github.com/containers/image";
-    fetch = {
-      type = "git";
-      url = "https://github.com/containers/image";
-      rev =  "2e4f799f5eba49a2498d2793cfb2a4bc823ca3f6";
-      sha256 = "0b9symgbkd2vgvp7mfpz1l03i2zivwbc5ycccwv78b1ikk9m6b75";
-    };
-  }
-  {
-    goPackagePath  = "github.com/containers/storage";
-    fetch = {
-      type = "git";
-      url = "https://github.com/containers/storage";
-      rev =  "88d80428f9b146f8f9fe7e2e8cc8688a5aae1a4e";
-      sha256 = "13fagjisbg55dhgjd72h0hiy6jfg8ggkcnjl5haqj13c2gkf6sam";
-    };
-  }
-  {
-    goPackagePath  = "github.com/coreos/go-iptables";
-    fetch = {
-      type = "git";
-      url = "https://github.com/coreos/go-iptables";
-      rev =  "b5b1876b170881a8259f036445ee89c8669db386";
-      sha256 = "1s1c04x47pk3168606x4vkg4avs8a7m407hpha8py1xni08cgb6m";
-    };
-  }
-  {
-    goPackagePath  = "github.com/coreos/go-systemd";
-    fetch = {
-      type = "git";
-      url = "https://github.com/coreos/go-systemd";
-      rev =  "39ca1b05acc7ad1220e09f133283b8859a8b71ab";
-      sha256 = "1kzqrrzqspa5qm7kwslxl3m16lqzns23c24rv474ajzwmj3ixmx1";
-    };
-  }
-  {
-    goPackagePath  = "github.com/cpuguy83/go-md2man";
-    fetch = {
-      type = "git";
-      url = "https://github.com/cpuguy83/go-md2man";
-      rev =  "20f5889cbdc3c73dbd2862796665e7c465ade7d1";
-      sha256 = "1w22dfdamsq63b5rvalh9k2y7rbwfkkjs7vm9vd4a13h2ql70lg2";
-    };
-  }
-  {
-    goPackagePath  = "github.com/d2g/dhcp4";
-    fetch = {
-      type = "git";
-      url = "https://github.com/d2g/dhcp4";
-      rev =  "a1d1b6c41b1ce8a71a5121a9cee31809c4707d9c";
-      sha256 = "191hzw6yqzkm042h6miyycq3g0zrhqjhhpl27f8vhwzp4wanasiz";
-    };
-  }
-  {
-    goPackagePath  = "github.com/d2g/dhcp4client";
-    fetch = {
-      type = "git";
-      url = "https://github.com/d2g/dhcp4client";
-      rev =  "e612998962035b93ba16cfd1ad2f3221985c1b8c";
-      sha256 = "1612wh99fblc9ashmm6mjc9110fhal95z0mn9qn7av3px13yd9fs";
-    };
-  }
-  {
-    goPackagePath  = "github.com/docker/distribution";
-    fetch = {
-      type = "git";
-      url = "https://github.com/docker/distribution";
-      rev =  "749f6afb4572201e3c37325d0ffedb6f32be8950";
-      sha256 = "05jn2wvikyw0pbmi74w5axr0zgxn5y3ynn9rhsq87rmwqj7raxhd";
-    };
-  }
-  {
-    goPackagePath  = "github.com/docker/docker";
-    fetch = {
-      type = "git";
-      url = "https://github.com/docker/docker";
-      rev =  "da99009bbb1165d1ac5688b5c81d2f589d418341";
-      sha256 = "02hhx7s8vm45rcl2mx9xamkncl2pb6qhsmz35mffbg4n6l5rn5x5";
-    };
-  }
-  {
-    goPackagePath  = "github.com/docker/docker-credential-helpers";
-    fetch = {
-      type = "git";
-      url = "https://github.com/docker/docker-credential-helpers";
-      rev =  "d68f9aeca33f5fd3f08eeae5e9d175edf4e731d1";
-      sha256 = "1ff829h5p1j6qiivjvnwyiybrff3dddv1ij71nz5whmgavdqgd49";
-    };
-  }
-  {
-    goPackagePath  = "github.com/docker/go-connections";
-    fetch = {
-      type = "git";
-      url = "https://github.com/docker/go-connections";
-      rev =  "3ede32e2033de7505e6500d6c868c2b9ed9f169d";
-      sha256 = "0v1pkr8apwmhyzbjfriwdrs1ihlk6pw7izm57r24mf9jdmg3fyb0";
-    };
-  }
-  {
-    goPackagePath  = "github.com/docker/go-metrics";
-    fetch = {
-      type = "git";
-      url = "https://github.com/docker/go-metrics";
-      rev =  "399ea8c73916000c64c2c76e8da00ca82f8387ab";
-      sha256 = "0najfy92fq05b330cnjk5b326yi7dnnmvzfk6g5lsa1fci78yzw4";
-    };
-  }
-  {
-    goPackagePath  = "github.com/docker/go-units";
-    fetch = {
-      type = "git";
-      url = "https://github.com/docker/go-units";
-      rev =  "47565b4f722fb6ceae66b95f853feed578a4a51c";
-      sha256 = "0npxsb3pp89slwf4a73fxm20hykad8xggij6i6hcd5jy19bjrd93";
-    };
-  }
-  {
-    goPackagePath  = "github.com/docker/libtrust";
-    fetch = {
-      type = "git";
-      url = "https://github.com/docker/libtrust";
-      rev =  "aabc10ec26b754e797f9028f4589c5b7bd90dc20";
-      sha256 = "1lwslbggzc2b0c4wxl5pn6i2nfgz5jz8f7s7vnid9mrlsk59h7s1";
-    };
-  }
-  {
-    goPackagePath  = "github.com/ghodss/yaml";
-    fetch = {
-      type = "git";
-      url = "https://github.com/ghodss/yaml";
-      rev =  "0ca9ea5df5451ffdf184b4428c902747c2c11cd7";
-      sha256 = "0skwmimpy7hlh7pva2slpcplnm912rp3igs98xnqmn859kwa5v8g";
-    };
-  }
-  {
-    goPackagePath  = "github.com/globalsign/mgo";
-    fetch = {
-      type = "git";
-      url = "https://github.com/globalsign/mgo";
-      rev =  "113d3961e7311526535a1ef7042196563d442761";
-      sha256 = "0m05ay993vv2jkc46bbdnq371s5jc0an2cycsj7p3b6lmv84jk9f";
-    };
-  }
-  {
-    goPackagePath  = "github.com/godbus/dbus";
-    fetch = {
-      type = "git";
-      url = "https://github.com/godbus/dbus";
-      rev =  "a389bdde4dd695d414e47b755e95e72b7826432c";
-      sha256 = "1ckvg15zdsgmbn4mi36cazkb407ixc9mmyf7vwj8b8wi3d00rgn9";
-    };
-  }
-  {
-    goPackagePath  = "github.com/gogo/protobuf";
-    fetch = {
-      type = "git";
-      url = "https://github.com/gogo/protobuf";
-      rev =  "1adfc126b41513cc696b209667c8656ea7aac67c";
-      sha256 = "1j7azzlnihcvnd1apw5zr0bz30h7n0gyimqqkgc76vzb1n5dpi7m";
-    };
-  }
-  {
-    goPackagePath  = "github.com/golang/protobuf";
-    fetch = {
-      type = "git";
-      url = "https://github.com/golang/protobuf";
-      rev =  "b4deda0973fb4c70b50d226b1af49f3da59f5265";
-      sha256 = "0ya4ha7m20bw048m1159ppqzlvda4x0vdprlbk5sdgmy74h3xcdq";
-    };
-  }
-  {
-    goPackagePath  = "github.com/gorilla/context";
-    fetch = {
-      type = "git";
-      url = "https://github.com/gorilla/context";
-      rev =  "08b5f424b9271eedf6f9f0ce86cb9396ed337a42";
-      sha256 = "03p4hn87vcmfih0p9w663qbx9lpsf7i7j3lc7yl7n84la3yz63m4";
-    };
-  }
-  {
-    goPackagePath  = "github.com/gorilla/mux";
-    fetch = {
-      type = "git";
-      url = "https://github.com/gorilla/mux";
-      rev =  "e3702bed27f0d39777b0b37b664b6280e8ef8fbf";
-      sha256 = "0pvzm23hklxysspnz52mih6h1q74vfrdhjfm1l3sa9r8hhqmmld2";
-    };
-  }
-  {
-    goPackagePath  = "github.com/gorilla/websocket";
-    fetch = {
-      type = "git";
-      url = "https://github.com/gorilla/websocket";
-      rev =  "ea4d1f681babbce9545c9c5f3d5194a789c89f5b";
-      sha256 = "1bhgs2542qs49p1dafybqxfs2qc072xv41w5nswyrknwyjxxs2a1";
-    };
-  }
-  {
-    goPackagePath  = "github.com/hashicorp/errwrap";
-    fetch = {
-      type = "git";
-      url = "https://github.com/hashicorp/errwrap";
-      rev =  "7554cd9344cec97297fa6649b055a8c98c2a1e55";
-      sha256 = "0kmv0p605di6jc8i1778qzass18m0mv9ks9vxxrfsiwcp4la82jf";
-    };
-  }
-  {
-    goPackagePath  = "github.com/hashicorp/go-multierror";
-    fetch = {
-      type = "git";
-      url = "https://github.com/hashicorp/go-multierror";
-      rev =  "b7773ae218740a7be65057fc60b366a49b538a44";
-      sha256 = "09904bk7ac6qs9dgiv23rziq9h3makb9qg4jvxr71rlydsd7psfd";
-    };
-  }
-  {
-    goPackagePath  = "github.com/inconshreveable/mousetrap";
-    fetch = {
-      type = "git";
-      url = "https://github.com/inconshreveable/mousetrap";
-      rev =  "76626ae9c91c4f2a10f34cad8ce83ea42c93bb75";
-      sha256 = "1mn0kg48xkd74brf48qf5hzp0bc6g8cf5a77w895rl3qnlpfw152";
-    };
-  }
-  {
-    goPackagePath  = "github.com/j-keck/arping";
-    fetch = {
-      type = "git";
-      url = "https://github.com/j-keck/arping";
-      rev =  "2cf9dc699c5640a7e2c81403a44127bf28033600";
-      sha256 = "1bid8mpx3j4546ni0a6q5xyz7hb854g95qnxqmg5jzs9vrcird3c";
-    };
-  }
-  {
-    goPackagePath  = "github.com/kubernetes-sigs/cri-o";
-    fetch = {
-      type = "git";
-      url = "https://github.com/kubernetes-sigs/cri-o";
-      rev =  "8afc34092907d146906fcc31af112b2b46e7b5cd";
-      sha256 = "0ghcjvk7grdcwb1936mnj56a7rla804glfknid9kmr3kgny3yi43";
-    };
-  }
-  {
-    goPackagePath  = "github.com/magiconair/properties";
-    fetch = {
-      type = "git";
-      url = "https://github.com/magiconair/properties";
-      rev =  "c2353362d570a7bfa228149c62842019201cfb71";
-      sha256 = "1a10362wv8a8qwb818wygn2z48lgzch940hvpv81hv8gc747ajxn";
-    };
-  }
-  {
-    goPackagePath  = "github.com/mattn/go-runewidth";
-    fetch = {
-      type = "git";
-      url = "https://github.com/mattn/go-runewidth";
-      rev =  "9e777a8366cce605130a531d2cd6363d07ad7317";
-      sha256 = "0vkrfrz3fzn5n6ix4k8s0cg0b448459sldq8bp4riavsxm932jzb";
-    };
-  }
-  {
-    goPackagePath  = "github.com/mattn/go-shellwords";
-    fetch = {
-      type = "git";
-      url = "https://github.com/mattn/go-shellwords";
-      rev =  "02e3cf038dcea8290e44424da473dd12be796a8a";
-      sha256 = "1pg7pl25wvpl2dbpyrv9p1r7prnqimxlf6136vn0dfm54j2x4mnr";
-    };
-  }
-  {
-    goPackagePath  = "github.com/matttproud/golang_protobuf_extensions";
-    fetch = {
-      type = "git";
-      url = "https://github.com/matttproud/golang_protobuf_extensions";
-      rev =  "c12348ce28de40eed0136aa2b644d0ee0650e56c";
-      sha256 = "1d0c1isd2lk9pnfq2nk0aih356j30k3h1gi2w0ixsivi5csl7jya";
-    };
-  }
-  {
-    goPackagePath  = "github.com/mtrmac/gpgme";
-    fetch = {
-      type = "git";
-      url = "https://github.com/mtrmac/gpgme";
-      rev =  "b2432428689ca58c2b8e8dea9449d3295cf96fc9";
-      sha256 = "0hs9gfwf3cmnvmmxb485icwlv8h8xnny3p52bj7qwv251pvwsnaf";
-    };
-  }
-  {
-    goPackagePath  = "github.com/opencontainers/go-digest";
-    fetch = {
-      type = "git";
-      url = "https://github.com/opencontainers/go-digest";
-      rev =  "279bed98673dd5bef374d3b6e4b09e2af76183bf";
-      sha256 = "01gc7fpn8ax429024p2fcx3yb18axwz5bjf2hqxlii1jbsgw4bh9";
-    };
-  }
-  {
-    goPackagePath  = "github.com/opencontainers/image-spec";
-    fetch = {
-      type = "git";
-      url = "https://github.com/opencontainers/image-spec";
-      rev =  "e562b04403929d582d449ae5386ff79dd7961a11";
-      sha256 = "0j24nk975di8hcv6ycn2p2hhw1xdiy4bpxamr6wn12k21kadlp7s";
-    };
-  }
-  {
-    goPackagePath  = "github.com/opencontainers/image-tools";
-    fetch = {
-      type = "git";
-      url = "https://github.com/sylabs/image-tools";
-      rev =  "2814f498056809a9d5baaf76d1d82312180a5888";
-      sha256 = "0q3ljb51df5hc58rhp5xni2gsy3gkxn47d9dwyfcffnq8kpf9d8a";
-    };
-  }
-  {
-    goPackagePath  = "github.com/opencontainers/runc";
-    fetch = {
-      type = "git";
-      url = "https://github.com/opencontainers/runc";
-      rev =  "baf6536d6259209c3edfa2b22237af82942d3dfa";
-      sha256 = "09fm7f1k4lvx8v3crqb0cli1x2brlz8ka7f7qa8d2sb6ln58h7w7";
-    };
-  }
-  {
-    goPackagePath  = "github.com/opencontainers/runtime-spec";
-    fetch = {
-      type = "git";
-      url = "https://github.com/opencontainers/runtime-spec";
-      rev =  "5806c35637336642129d03657419829569abc5aa";
-      sha256 = "13vw1b3j9sx7d5fr3w3jdg137nnqcr50fqchq8z8nf6s18lkhj93";
-    };
-  }
-  {
-    goPackagePath  = "github.com/opencontainers/runtime-tools";
-    fetch = {
-      type = "git";
-      url = "https://github.com/opencontainers/runtime-tools";
-      rev =  "1c243a8a8eb44d491790798afc9b634c6f6a6380";
-      sha256 = "1ll5wrbn84yb2l7k6hpwwj06wywib7ar4z1bhh1rc5h9xajng7jq";
-    };
-  }
-  {
-    goPackagePath  = "github.com/opencontainers/selinux";
-    fetch = {
-      type = "git";
-      url = "https://github.com/opencontainers/selinux";
-      rev =  "ba1aefe8057f1d0cfb8e88d0ec1dc85925ef987d";
-      sha256 = "1n283j7rsim7gysm91x99c41d7vnsjsgfm4dy11fnzpkpzfiksq5";
-    };
-  }
-  {
-    goPackagePath  = "github.com/pelletier/go-toml";
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-]
\ No newline at end of file
+[]