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Fix structure of recipe #15249

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May 11, 2019
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37 changes: 20 additions & 17 deletions recipes/cluster-picker/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,29 +1,32 @@
about:
home: http://hiv.bio.ed.ac.uk/software.html
license: GPLv3
summary: The Cluster Picker identifies clusters in newick-formatted trees
containing thousands of sequences within a few minutes. Cut-offs for
within cluster genetic distance and bootstrap support are selected by
the user.

requirements:
run:
- java-jdk
{% set name = "ClusterPicker" %}
{% set version = "1.2.3" %}
{% set sha256 = "a8a3bb5107c54d2621b974e5953ff7f2c03352fb225954ef43533829a4d72948" %}

package:
name: cluster-picker
version: 1.2.3

build:
number: 1
name: "{{ name|lower }}"
version: "{{ version }}"

source:
url: http://hiv.bio.ed.ac.uk/clusterPicker/ClusterPicker_1.2.3.jar
md5: 95c19264a268f2522fccc520f52989b6
sha256: {{ sha256 }}

build:
noarch: generic
number: 2

requirements:
run:
- openjdk >=6

test:
commands:
- which cluster-picker
- echo -e ">seq1\nATTA\n>seq2\nATTA\n>seq3\nATTA\n>seq4\nATTA" > dummy.fasta
- echo "(((seq1:0.001,seq2:0.002):0.001,seq3:0.005):0.004,seq4:0.003):0.001;" > dummy.nwk
- echo -e "y\ny\ny\ny\ny\n" | cluster-picker dummy.fasta dummy.nwk

about:
home: http://hiv.bio.ed.ac.uk/software.html
license: GPLv3
license_family: GPL
summary: "The Cluster Picker identifies clusters in newick-formatted trees containing thousands of sequences within a few minutes."
32 changes: 21 additions & 11 deletions recipes/opsin/1.4.0/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,22 +1,33 @@
about:
home: https://bitbucket.org/dan2097/opsin/
license: Artistic License 2.0
summary: OPSIN is a Java(1.6+) library for IUPAC name-to-structure conversion offering high recall and precision on organic chemical nomenclature.
{% set name = "opsin" %}
{% set version = "1.4.0" %}
{% set sha256 = "01f119afd2702390f588826bd79740eb714a68ee6229f8062f9b56490199e894" %}

package:
name: opsin
version: 1.4.0
build:
number: 2
name: "{{ name|lower }}"
version: "{{ version }}"

source:
url: https://bitbucket.org/dan2097/opsin/downloads/opsin-1.4.0-jar-with-dependencies.jar
sha256: {{ sha256 }}

build:
noarch: generic
number: 3

requirements:
build:
run:
- java-jdk >=6
- openjdk >=6

test:
commands:
- opsin --help
- opsin -Xms512m -Xmx1g --help

about:
home: https://bitbucket.org/dan2097/opsin/
license: Artistic License 2.0
summary: "OPSIN is a Java(1.6+) library for IUPAC name-to-structure conversion offering high recall and precision on organic chemical nomenclature."

extra:
notes: |
Opsin is Java program that comes with a custom wrapper shell script.
Expand All @@ -25,4 +36,3 @@ extra:
specify these values directly after your binaries. If you have _JAVA_OPTIONS
set globally this will take precedence.
For example run opsin with "opsin -Xms512m -Xmx1g --help"
34 changes: 22 additions & 12 deletions recipes/opsin/2.1.0/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,28 +1,38 @@
about:
home: https://bitbucket.org/dan2097/opsin/
license: Artistic License 2.0
summary: OPSIN is a Java(1.6+) library for IUPAC name-to-structure conversion offering high recall and precision on organic chemical nomenclature.
{% set name = "opsin" %}
{% set version = "2.1.0" %}
{% set sha256 = "35462464d0440019ce2da26e3b8fcbb4757997139969c1662bc1f54b760a4785" %}

package:
name: opsin
version: 2.1.0
build:
number: 2
name: "{{ name|lower }}"
version: "{{ version }}"

source:
url: https://bitbucket.org/dan2097/opsin/downloads/opsin-2.1.0-jar-with-dependencies.jar
sha256: {{ sha256 }}

build:
noarch: generic
number: 3

requirements:
build:
run:
- java-jdk >=6
- openjdk >=6

test:
commands:
- opsin --help
- opsin -Xms512m -Xmx1g --help

about:
home: https://bitbucket.org/dan2097/opsin/
license: Artistic License 2.0
summary: "OPSIN is a Java(1.6+) library for IUPAC name-to-structure conversion offering high recall and precision on organic chemical nomenclature."

extra:
notes: |
Opsin is Java program that comes with a custom wrapper shell script.
This shell wrapper is called "opsin" and is on $PATH by default. By default
"-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can
specify these values directly after your binaries. If you have _JAVA_OPTIONS
set globally this will take precedence.
sFor example run opsin with "opsin -Xms512m -Xmx1g --help"
For example run opsin with "opsin -Xms512m -Xmx1g --help"
33 changes: 21 additions & 12 deletions recipes/opsin/2.4.0/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,29 +1,38 @@
about:
home: https://bitbucket.org/dan2097/opsin/
license: Artistic License 2.0
summary: OPSIN is a Java(1.6+) library for IUPAC name-to-structure conversion offering high recall and precision on organic chemical nomenclature.
{% set name = "opsin" %}
{% set version = "2.4.0" %}
{% set sha256 = "3e8a276a378e09c1536f52e09dc8028d648c881277b9146c991bf6b9ec231d88" %}

package:
name: opsin
version: 2.4.0
build:
number: 0
name: "{{ name|lower }}"
version: "{{ version }}"

source:
url: https://bitbucket.org/dan2097/opsin/downloads/opsin-2.4.0-jar-with-dependencies.jar
sha256: 3e8a276a378e09c1536f52e09dc8028d648c881277b9146c991bf6b9ec231d88
sha256: {{ sha256 }}

build:
noarch: generic
number: 1

requirements:
build:
run:
- openjdk >=6

test:
commands:
- opsin --help
- opsin -Xms512m -Xmx1g --help

about:
home: https://bitbucket.org/dan2097/opsin/
license: Artistic License 2.0
summary: "OPSIN is a Java(1.6+) library for IUPAC name-to-structure conversion offering high recall and precision on organic chemical nomenclature."

extra:
notes: |
Opsin is Java program that comes with a custom wrapper shell script.
This shell wrapper is called "opsin" and is on $PATH by default. By default
"-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can
specify these values directly after your binaries. If you have _JAVA_OPTIONS
set globally this will take precedence.
sFor example run opsin with "opsin -Xms512m -Xmx1g --help"
For example run opsin with "opsin -Xms512m -Xmx1g --help"