pb-falconc-0.0.1

recipes/pb-falconc/build.sh

@@ -0,0 +1,49 @@
+#!/bin/bash
+set -vexu -o pipefail
+
+NIM_VERSION=devel
+# devel, b/c branches are missing.
+#NIM_VERSION=v0.20.2
+#NIMBLE_VERSION=v0.9.0
+export base=$(pwd)
+
+# Install nim
+git clone -b $NIM_VERSION --depth 1 git://github.com/nim-lang/nim nim-$NIM_VERSION/
+cd nim-$NIM_VERSION
+git clone                 --depth 1 git://github.com/nim-lang/csources csources/
+
+cd csources
+# Fix compiler references to use conda set CC
+# https://github.com/brentp/mosdepth/blob/master/scripts/install.sh
+export LINKER=$CC
+sed -i.bak '/^CC=/s/^/#/g' build.sh
+sed -i.bak '/^LINKER=/s/^/#/g' build.sh
+sh build.sh
+cd ..
+rm -rf csources
+bin/nim c koch
+./koch boot -d:release
+
+export PATH=$base/nim-$NIM_VERSION/bin
+
+#git clone -b $NIMBLE_VERSION --depth 1 git://github.com/nim-lang/nimble.git
+#cd nimble
+#nim c src/nimble
+
+which nim
+nim -v
+
+cd $base
+ls -larth
+
+cd $base
+
+export NIMBLEDIR=$(pwd)/.nimble
+#nimble install -y
+make build
+
+#mkdir -p $PREFIX/bin
+#chmod a+x falconc
+#cp falconc $PREFIX/bin
+ls -larth src
+make install

recipes/pb-falconc/meta.yaml

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+{% set version = "0.1.1" %}
+{% set sha256hash = "152b1f50ee9ba375099cd739928a9c78c25c3b7127314f15d06667de3c5b979d" %}
+
+package:
+  name: pb-falconc
+  version: {{ version }}
+
+source:
+  url: https://github.com/bio-nim/nim-pb/archive/8d5aa9fecedc40d3dd220d01eca8942ec8ba2eb1.tar.gz
+  sha256: {{ sha256hash }}
+
+build:
+  number: 0
+  skip: True  # [not linux]
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+  host:
+    - pcre
+    - htslib
+  run:
+    - pcre
+    - htslib
+
+test:
+  commands:
+    - falconc -h
+
+about:
+  home: 'https://github.com/PacificBiosciences/pbbioconda'
+  license: "BSD 3-Clause Clear License"
+  summary: "C utilities for PacBio assembly (pb-falcon etc.)"
+  authors:
+    - pb-cdunn
+    - isovic
+    - zkronenberg