Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Dinucleotide patterns analysis tools v1.0 #11245

Merged
merged 2 commits into from
Oct 6, 2018
Merged

Dinucleotide patterns analysis tools v1.0 #11245

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
abd8b6d
Dinucleotide patterns analysis tools v1.0
Oct 6, 2018
84c28ef
Lets try it, it seems to work locally for me.
bgruening Oct 6, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 14 additions & 0 deletions recipes/dnp-binstrings/build.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
#!/bin/bash

sed 's/CPROGNAME/binstrings/g' CMakeLists.template > CMakeLists.txt

mkdir -p build
cd build

SEQAN_INCLUDE_PATH="$CONDA_DEFAULT_ENV/include/"
CMAKE_PREFIX_PATH="$CONDA_DEFAULT_ENV/share/cmake/seqan"
cmake ../ -DCMAKE_PREFIX_PATH="$CMAKE_PREFIX_PATH" -DSEQAN_INCLUDE_PATH="$SEQAN_INCLUDE_PATH"

make
cp binstrings $PREFIX/bin

6 changes: 6 additions & 0 deletions recipes/dnp-binstrings/conda_build_config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
c_compiler:
- gcc # [linux]
- clang # [osx]
cxx_compiler:
- gxx # [linux]
- clangxx # [osx]
34 changes: 34 additions & 0 deletions recipes/dnp-binstrings/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
package:
name: binstrings
version: "1.0"

source:
url: https://github.com/erinijapranckeviciene/dnpatterntools/files/2450741/v1.0.tar.gz
sha256: 19c46d6bc6a1af70e5a2b4a051aab334026dc38c84b367ea9c445da3fdb21cfe

build:
number: 0

requirements:
build:
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- seqan-library
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Seqan should probably in the host section.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thank you for the comment. It was a journey... No. Seqan is C++ header only library. It matters only in compilation. But it depends on zlib and bzip2. The two should be in the host and run.

- cmake

host:
- zlib
- bzip2

run:
- zlib
- bzip2

test:
commands:
- binstrings --help

about:
home: https://github.com/erinijapranckeviciene/dnpatterntools
license: MIT
summary: "Convert fasta strings into dinucleotide binary indicator string as 00101..."
14 changes: 14 additions & 0 deletions recipes/dnp-corrprofile/build.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
#!/bin/bash

sed 's/CPROGNAME/corrprofile/g' CMakeLists.template > CMakeLists.txt

mkdir -p build
cd build

SEQAN_INCLUDE_PATH="$CONDA_DEFAULT_ENV/include/"
CMAKE_PREFIX_PATH="$CONDA_DEFAULT_ENV/share/cmake/seqan"
cmake ../ -DCMAKE_PREFIX_PATH="$CMAKE_PREFIX_PATH" -DSEQAN_INCLUDE_PATH="$SEQAN_INCLUDE_PATH"

make
cp corrprofile $PREFIX/bin

6 changes: 6 additions & 0 deletions recipes/dnp-corrprofile/conda_build_config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
c_compiler:
- gcc # [linux]
- clang # [osx]
cxx_compiler:
- gxx # [linux]
- clangxx # [osx]
34 changes: 34 additions & 0 deletions recipes/dnp-corrprofile/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
package:
name: corrprofile
version: "1.0"

source:
url: https://github.com/erinijapranckeviciene/dnpatterntools/files/2450741/v1.0.tar.gz
sha256: 19c46d6bc6a1af70e5a2b4a051aab334026dc38c84b367ea9c445da3fdb21cfe

build:
number: 0

requirements:
build:
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- seqan-library
- cmake

host:
- zlib
- bzip2

run:
- zlib
- bzip2

test:
commands:
- corrprofile --help

about:
home: https://github.com/erinijapranckeviciene/dnpatterntools
license: MIT
summary: "Profile of correlations between the patterns of dinucleotide frequency on forward and reverse strands"
14 changes: 14 additions & 0 deletions recipes/dnp-diprofile/build.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
#!/bin/bash

sed 's/CPROGNAME/diprofile/g' CMakeLists.template > CMakeLists.txt

mkdir -p build
cd build

SEQAN_INCLUDE_PATH="$CONDA_DEFAULT_ENV/include/"
CMAKE_PREFIX_PATH="$CONDA_DEFAULT_ENV/share/cmake/seqan"
cmake ../ -DCMAKE_PREFIX_PATH="$CMAKE_PREFIX_PATH" -DSEQAN_INCLUDE_PATH="$SEQAN_INCLUDE_PATH"

make
cp diprofile $PREFIX/bin

6 changes: 6 additions & 0 deletions recipes/dnp-diprofile/conda_build_config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
c_compiler:
- gcc # [linux]
- clang # [osx]
cxx_compiler:
- gxx # [linux]
- clangxx # [osx]
34 changes: 34 additions & 0 deletions recipes/dnp-diprofile/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
package:
name: diprofile
version: "1.0"

source:
url: https://github.com/erinijapranckeviciene/dnpatterntools/files/2450741/v1.0.tar.gz
sha256: 19c46d6bc6a1af70e5a2b4a051aab334026dc38c84b367ea9c445da3fdb21cfe

build:
number: 0

requirements:
build:
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- seqan-library
- cmake

host:
- zlib
- bzip2

run:
- zlib
- bzip2

test:
commands:
- diprofile --help

about:
home: https://github.com/erinijapranckeviciene/dnpatterntools
license: MIT
summary: "Dinucleotide frequency of occurrence in a batch of fasta sequences"
4 changes: 4 additions & 0 deletions recipes/dnp-fourier/build.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
#!/bin/bash

make fourier
cp fourier $PREFIX/bin
28 changes: 28 additions & 0 deletions recipes/dnp-fourier/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
package:
name: fourier
version: "1.0"

source:
url: https://github.com/erinijapranckeviciene/dnpatterntools/files/2450741/v1.0.tar.gz
sha256: 19c46d6bc6a1af70e5a2b4a051aab334026dc38c84b367ea9c445da3fdb21cfe

build:
number: 0

requirements:
build:
- {{ compiler('c') }}
- {{ compiler('cxx') }}

host:

run:

test:
commands:
- fourier --help

about:
home: https://github.com/erinijapranckeviciene/dnpatterntools
license: MIT
summary: "Periodogram of dinucleotide frequency pattern"