Merge pull request #8 from bioconda/master

bioconda master

recipes/jpeg/build.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+./configure --prefix=$PREFIX
+make
+make install

recipes/jpeg/meta.yaml

@@ -0,0 +1,16 @@
+package:
+  name: jpeg
+  version: 9b
+
+source:
+  fn: jpegsrc.v9b.tar.gz
+  url: http://www.ijg.org/files/jpegsrc.v9b.tar.gz
+  md5: 6a9996ce116ec5c52b4870dbcd6d3ddb
+
+build:
+  number: 0
+
+about:
+  home: http://www.ijg.org/
+  license: Custom free software license
+summary: read/write jpeg COM, EXIF, IPTC medata

recipes/libgd/meta.yaml

@@ -3,24 +3,27 @@ package:
   version: 2.2.3
 
 build:
-  number: 1
+  number: 2
 
 requirements:
   build:
     - gcc # [not osx]
     - llvm # [osx]
     - zlib
     - freetype
-    - jpeg
+    - jpeg >=9* # use recent libjpeg
     - libpng
     - libtiff
+    - fontconfig # for libfontconfig.so
+
   run:
     - libgcc # [not osx]
     - zlib
     - freetype
-    - jpeg
+    - jpeg >=9* # use recent libjpeg
     - libpng
     - libtiff
+    - fontconfig # for libfontconfig.so
 
 source:
   fn: libgd-2.2.3.tar.gz

recipes/pipmir/build.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+set -eu -o pipefail
+
+PKG_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
+mkdir -p $PKG_HOME
+mkdir -p $PREFIX/bin
+
+cd $SRC_DIR
+
+cp -r  PIPmiR src README $PKG_HOME/.
+chmod +x $PKG_HOME/PIPmiR
+ln -s $PKG_HOME/PIPmiR $PREFIX/bin/PIPmiR

recipes/pipmir/meta.yaml

@@ -0,0 +1,33 @@
+package:
+  name: pipmir
+  version: 1.1
+
+source:
+  fn: PIPmiR_v1_1b_executable.tar.gz
+  url: https://ohlerlab.mdc-berlin.de/files/duke/PIPmiR/PIPmiR_v1_1b_executable.tar.gz
+  md5: 4103f0a148e4cc0217c616c1606f11c5
+
+build:
+  skip: True  # [not linux]
+  number: 0
+
+requirements:
+  build:
+    - java-jdk
+    - samtools
+    - viennarna
+  run:
+    - java-jdk
+    - samtools
+    - viennarna
+
+test:
+  commands:
+    - PIPmiR
+
+about:
+  home: https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/
+  license: 'PIPmiR is provided for academic use only,
+  if you wish to use it in another setting please contact Uwe Ohler.'
+  summary: 'We developed the PIPmiR algorithm to identify novel plant miRNA
+  genes from a combination of deep sequencing data and genomic features.'

recipes/r-inlinedocs/build.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# R refuses to build packages that mark themselves as Priority: Recommended
+mv DESCRIPTION DESCRIPTION.old
+grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+
+$R CMD INSTALL --build .
+
+# Add more build steps here, if they are necessary.
+
+# See
+# http://docs.continuum.io/conda/build.html
+# for a list of environment variables that are set during the build process.

recipes/r-inlinedocs/meta.yaml

@@ -0,0 +1,64 @@
+package:
+  name: r-inlinedocs
+  version: "2013.9.3"
+
+source:
+  fn: inlinedocs_2013.9.3.tar.gz
+  url:
+    - http://cran.r-project.org/src/contrib/inlinedocs_2013.9.3.tar.gz
+    - http://cran.r-project.org/src/contrib/Archive/inlinedocs/inlinedocs_2013.9.3.tar.gz
+  md5: 16de1fef5c76f458c06d438fba67791f
+
+build:
+  # number: 1
+
+  # This is required to make R link correctly on Linux.
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+
+requirements:
+  build:
+    - r
+
+  run:
+    - r
+
+test:
+  commands:
+    # You can put additional test commands to be run here.
+    - $R -e "library('inlinedocs')"
+
+about:
+  home: http://inlinedocs.r-forge.r-project.org
+  license: GPL-2 | GPL-3
+  summary: Generates Rd files from R source code with comments. The main features of the default
+    syntax are that (1) docs are defined in comments near the relevant code, (2) function
+    argument names are not repeated in comments, and (3) examples are defined in R code,
+    not comments. It is also easy to define a new syntax.
+  license_family: GPL3
+
+# The original CRAN metadata for this package was:
+
+# Package: inlinedocs
+# Title: Convert inline comments to documentation
+# Type: Package
+# Version: 2013.9.3
+# Authors@R: c(person("Toby Dylan","Hocking",role=c("aut","cre"), email="[email protected]"), person("Keith","Ponting",role="aut"), person("Thomas","Wutzler",role="aut"), person("Philippe","Grosjean",role="aut"), person("Markus","MAzller",role="aut"), person("R Core Team",role=c("ctb","cph")))
+# Description: Generates Rd files from R source code with comments. The main features of the default syntax are that (1) docs are defined in comments near the relevant code, (2) function argument names are not repeated in comments, and (3) examples are defined in R code, not comments. It is also easy to define a new syntax.
+# URL: http://inlinedocs.r-forge.r-project.org
+# Depends: methods, utils, R (>= 2.9)
+# License: GPL-2 | GPL-3
+# LazyLoad: yes
+# Encoding: UTF-8
+# Packaged: 2013-09-03 07:45:07 UTC; toby
+# Author: Toby Dylan Hocking [aut, cre], Keith Ponting [aut], Thomas Wutzler [aut], Philippe Grosjean [aut], Markus MAzller [aut], R Core Team [ctb, cph]
+# Maintainer: Toby Dylan Hocking <[email protected]>
+# NeedsCompilation: no
+# Repository: CRAN
+# Date/Publication: 2013-09-03 13:04:14
+
+# See
+# http://docs.continuum.io/conda/build.html for
+# more information about meta.yaml

recipes/r-penalized/build.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# R refuses to build packages that mark themselves as Priority: Recommended
+mv DESCRIPTION DESCRIPTION.old
+grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+
+$R CMD INSTALL --build .
+
+# Add more build steps here, if they are necessary.
+
+# See
+# http://docs.continuum.io/conda/build.html
+# for a list of environment variables that are set during the build process.

recipes/r-penalized/meta.yaml

@@ -0,0 +1,70 @@
+package:
+  name: r-penalized
+  version: "0.9.47"
+
+source:
+  fn: penalized_0.9-47.tar.gz
+  url:
+    - https://cran.r-project.org/src/contrib/penalized_0.9-47.tar.gz
+  md5: '13cf7400f8840317b1bbfc980d3f0333'
+
+build:
+  # This is required to make R link correctly on Linux.
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+    - r
+    - r-survival
+
+  run:
+    - r
+    - r-survival
+
+test:
+  commands:
+    # You can put additional test commands to be run here.
+    - $R -e "library('penalized')" 
+
+
+about:
+  home: https://cran.r-project.org/web/packages/penalized/index.html
+  license: GPL-2
+  summary: Fitting possibly high dimensional penalized regression models. The penalty structure 
+    can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a 
+    positivity constraint on the regression coefficients. The supported regression models are 
+    linear, logistic and Poisson regression and the Cox Proportional Hazards model. 
+    Cross-validation routines allow optimization of the tuning parameters.
+  license_family: GPL2
+
+# The original CRAN metadata for this package was:
+
+# Package: penalized
+# Version: 0.9-47
+# Date: 2016-05-26
+# Title: L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation
+#         in GLMs and in the Cox Model
+# Author: Jelle Goeman, Rosa Meijer, Nimisha Chaturvedi
+# Maintainer: Jelle Goeman <[email protected]>
+# Depends: R (>= 2.10.0), survival, methods
+# Imports:
+# Suggests: globaltest
+# Description: Fitting possibly high dimensional penalized
+#         regression models. The penalty structure can be any combination
+#         of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a
+#         positivity constraint on the regression coefficients. The
+#         supported regression models are linear, logistic and Poisson
+#         regression and the Cox Proportional Hazards model.
+#         Cross-validation routines allow optimization of the tuning
+#         parameters.
+# License: GPL (>= 2)
+# Collate: onattach.R penfit.R breslow.R penalized.R core.R checkinput.R
+#         cvl.R contrasts.R Brent.R plotpath.R cox.R logit.R linear.R
+#         poisson.R
+# LazyLoad: yes
+# Repository: CRAN
+# Date/Publication: 2016-05-27 18:08:55
+# Packaged: 2016-05-27 11:43:08 UTC; jjgoeman
+# NeedsCompilation: no