Add py-pipits 2.4 (#12074)

* Add py-pipits 2.4

* Flake8 fix

4 files changed, 81 insertions, 8 deletions

diff --git a/var/spack/repos/builtin/packages/py-pipits/package.py b/var/spack/repos/builtin/packages/py-pipits/package.py
index ac88278d20..b97ef7b61b 100644
--- a/var/spack/repos/builtin/packages/py-pipits/package.py
+++ b/var/spack/repos/builtin/packages/py-pipits/package.py
@@ -10,19 +10,29 @@ class PyPipits(PythonPackage):
     """Automated pipeline for analyses of fungal ITS from the Illumina"""
 
     homepage = "https://github.com/hsgweon/pipits"
-    url      = "https://github.com/hsgweon/pipits/archive/1.5.0.tar.gz"
+    url      = "https://github.com/hsgweon/pipits/archive/2.4.tar.gz"
 
+    version('2.4', sha256='b08a9d70ac6e5dd1c64d56b77384afd69e21e7d641b2fc4416feff862a2cd054')
     version('1.5.0', '3f9b52bd7ffbcdb96d7bec150275070a')
 
-    depends_on('python@:2.999', type=('build', 'run'))
+    # https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pipits/meta.yaml
+    depends_on('python@3:', type=('build', 'run'), when='@2:')
+    depends_on('python@:2', type=('build', 'run'), when='@:1')
+    depends_on('py-setuptools', type='build', when='@2:')
+    depends_on('py-pispino@1.1:', type=('build', 'run'), when='@2:')
+    depends_on('vsearch', type='run')
+    depends_on('fastx-toolkit', type='run')
+    depends_on('hmmer', type='run')
+    depends_on('itsx', type='run')
     depends_on('py-biom-format', type=('build', 'run'))
+    depends_on('rdptools', type='run', when='@2:')
     depends_on('py-numpy', type=('build', 'run'))
-    depends_on('java', type=('build', 'run'))
-    depends_on('hmmer')
-    depends_on('fastx-toolkit')
-    depends_on('vsearch')
-    depends_on('itsx')
-    depends_on('rdp-classifier')
+    depends_on('py-pandas', type=('build', 'run'), when='@2:')
+    depends_on('py-progressbar2', type=('build', 'run'), when='@2:')
+    depends_on('py-requests', type=('build', 'run'), when='@2:')
+    depends_on('seqkit', type='run')
+    depends_on('java', type=('build', 'run'), when='@:1')
+    depends_on('rdp-classifier', type='run', when='@:1')
 
     resource(
         name='UNITE_retrained',
diff --git a/var/spack/repos/builtin/packages/py-pispino/package.py b/var/spack/repos/builtin/packages/py-pispino/package.py
new file mode 100644
index 0000000000..bcb3c04e38
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pispino/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPispino(PythonPackage):
+    """PISPINO (PIpits SPIN-Off tools)."""
+
+    homepage = "https://github.com/hsgweon/pispino"
+    url      = "https://github.com/hsgweon/pispino/archive/1.1.tar.gz"
+
+    version('1.1', sha256='8fb2e1c0ae38ecca7c637de9c0b655eb18fc67d7838ceb5a6902555ea12416c0')
+
+    # https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pispino/meta.yaml
+    depends_on('py-setuptools', type='build')
+    depends_on('vsearch', type='run')
+    depends_on('fastx-toolkit', type='run')
diff --git a/var/spack/repos/builtin/packages/rdptools/package.py b/var/spack/repos/builtin/packages/rdptools/package.py
new file mode 100644
index 0000000000..22644f6606
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rdptools/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Rdptools(MakefilePackage):
+    """Collection of commonly used RDP Tools for easy building."""
+
+    homepage = "https://github.com/rdpstaff/RDPTools"
+    url      = "https://github.com/rdpstaff/RDPTools/archive/2.0.2.tar.gz"
+
+    version('2.0.2', sha256='fc3d7f8129b45e602fc2c23e5e037a7f48c14d5a6b05c64f8c1d48e9767ac01d')
+
+    # https://github.com/bioconda/bioconda-recipes/blob/master/recipes/rdptools/meta.yaml
+    depends_on('java')
+    depends_on('ant')
+    depends_on('python')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/seqkit/package.py b/var/spack/repos/builtin/packages/seqkit/package.py
new file mode 100644
index 0000000000..2a58be05b6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/seqkit/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Seqkit(Package):
+    """A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
+    in Golang."""
+
+    homepage = "http://bioinf.shenwei.me/seqkit"
+    url      = "https://github.com/shenwei356/seqkit/releases/download/v0.10.1/seqkit_linux_amd64.tar.gz"
+
+    version('0.10.1', sha256='82f1c86dc4bd196403a56c2bf3ec063e5674a71777e68d940c4cc3d8411d2e9d')
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('seqkit', prefix.bin)