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author | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
---|---|---|
committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-chemistry/xia2 | |
download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip |
proj/gentoo: Initial commit
This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.
This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.
Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-chemistry/xia2')
-rw-r--r-- | sci-chemistry/xia2/Manifest | 6 | ||||
-rw-r--r-- | sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch | 61 | ||||
-rw-r--r-- | sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch | 61 | ||||
-rw-r--r-- | sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch | 61 | ||||
-rw-r--r-- | sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch | 61 | ||||
-rw-r--r-- | sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch | 28 | ||||
-rw-r--r-- | sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch | 28 | ||||
-rw-r--r-- | sci-chemistry/xia2/metadata.xml | 5 | ||||
-rw-r--r-- | sci-chemistry/xia2/xia2-0.3.1.0.ebuild | 59 | ||||
-rw-r--r-- | sci-chemistry/xia2/xia2-0.3.1.6.ebuild | 66 | ||||
-rw-r--r-- | sci-chemistry/xia2/xia2-0.3.1.7.ebuild | 66 | ||||
-rw-r--r-- | sci-chemistry/xia2/xia2-0.3.3.1.ebuild | 70 | ||||
-rw-r--r-- | sci-chemistry/xia2/xia2-0.3.3.3.ebuild | 70 | ||||
-rw-r--r-- | sci-chemistry/xia2/xia2-0.3.4.0.ebuild | 70 |
14 files changed, 712 insertions, 0 deletions
diff --git a/sci-chemistry/xia2/Manifest b/sci-chemistry/xia2/Manifest new file mode 100644 index 000000000000..e7fa594c3ec9 --- /dev/null +++ b/sci-chemistry/xia2/Manifest @@ -0,0 +1,6 @@ +DIST xia2-0.3.1.0.tar.bz2 3389906 SHA256 32f1866bc17b093cbf157ec7bc217e47d059957104b20c88ed1b5c3706fc7e28 +DIST xia2-0.3.1.6.tar.bz2 3464982 SHA256 fde814a763e6666a1618d01569c19d574f1bf71d754dc3960beeb13c35dd201f +DIST xia2-0.3.1.7.tar.bz2 3650285 SHA256 54beb26396c4b6ecb343544c777c2505238385f2127482d035d2c47b24a7fcf1 +DIST xia2-0.3.3.1.tar.bz2 3074989 SHA256 f1bf94cd9305f768fea1b541ac53d66917126e92620263a96f9c23923ec829c4 +DIST xia2-0.3.3.3.tar.bz2 2919316 SHA256 3cf09fcf9d2c0ea6d6cb8cf66a3c5af752b4345af6a882e2d398424cf3b4b0d3 +DIST xia2-0.3.4.0.tar.bz2 21404771 SHA256 20afe3d24c35446ef8c8944974d684229f053d3916e96e46766d8eefa4c5fabf diff --git a/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch new file mode 100644 index 000000000000..9d92af7e33ce --- /dev/null +++ b/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch @@ -0,0 +1,61 @@ +diff --git a/xia2-0.3.1.0/Applications/xia2find.py b/xia2-0.3.1.0/Applications/xia2find.py +index 1a3b0e2..e0b8a1e 100755 +--- a/xia2-0.3.1.0/Applications/xia2find.py ++++ b/xia2-0.3.1.0/Applications/xia2find.py +@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory + from Experts.FindImages import image2template_directory + + known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', +- 'osc', 'cbf', 'mar2000']] ++ 'osc', 'cbf', 'mar2000'] + known_sweeps = { } + + def is_image_name(file): +diff --git a/xia2-0.3.1.0/Experts/DRStrategyExpert.py b/xia2-0.3.1.0/Experts/DRStrategyExpert.py +index 28b1dc3..dba3ef7 100644 +--- a/xia2-0.3.1.0/Experts/DRStrategyExpert.py ++++ b/xia2-0.3.1.0/Experts/DRStrategyExpert.py +@@ -48,24 +48,24 @@ strategy_dict = { + 'default':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'default':{ + 'score':2, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} ++ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, + 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':2, + 'pipeline':{ +- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} ++ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, + 'depends-on':['xds', 'xscale']} + } +diff --git a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py +index 88f9218..5fb6f2a 100644 +--- a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py ++++ b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py +@@ -49,8 +49,8 @@ def Cad(DriverType = None): + self.add_command_line(hklin) + + self.set_task('Rewriting reflections %s => %s' % +- ` (os.path.split(hklin)[-1], +- ` os.path.split(self.getHklout())[-1])) ++ (os.path.split(hklin)[-1], ++ os.path.split(self.getHklout())[-1])) + + self.start() + diff --git a/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch new file mode 100644 index 000000000000..7770a53c4451 --- /dev/null +++ b/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch @@ -0,0 +1,61 @@ +diff --git a/xia2-0.3.1.6/Applications/xia2find.py b/xia2-0.3.1.6/Applications/xia2find.py +index 1a3b0e2..e0b8a1e 100755 +--- a/xia2-0.3.1.6/Applications/xia2find.py ++++ b/xia2-0.3.1.6/Applications/xia2find.py +@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory + from Experts.FindImages import image2template_directory + + known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', +- 'osc', 'cbf', 'mar2000']] ++ 'osc', 'cbf', 'mar2000'] + known_sweeps = { } + + def is_image_name(file): +diff --git a/xia2-0.3.1.6/Experts/DRStrategyExpert.py b/xia2-0.3.1.6/Experts/DRStrategyExpert.py +index 28b1dc3..dba3ef7 100644 +--- a/xia2-0.3.1.6/Experts/DRStrategyExpert.py ++++ b/xia2-0.3.1.6/Experts/DRStrategyExpert.py +@@ -48,24 +48,24 @@ strategy_dict = { + 'default':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'default':{ + 'score':2, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} ++ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, + 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':2, + 'pipeline':{ +- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} ++ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, + 'depends-on':['xds', 'xscale']} + } +diff --git a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py +index 88f9218..5fb6f2a 100644 +--- a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py ++++ b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py +@@ -49,8 +49,8 @@ def Cad(DriverType = None): + self.add_command_line(hklin) + + self.set_task('Rewriting reflections %s => %s' % +- ` (os.path.split(hklin)[-1], +- ` os.path.split(self.getHklout())[-1])) ++ (os.path.split(hklin)[-1], ++ os.path.split(self.getHklout())[-1])) + + self.start() + diff --git a/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch new file mode 100644 index 000000000000..ec8ada48aad1 --- /dev/null +++ b/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch @@ -0,0 +1,61 @@ +diff --git a/xia2-0.3.1.7/Applications/xia2find.py b/xia2-0.3.1.7/Applications/xia2find.py +index 1a3b0e2..e0b8a1e 100755 +--- a/xia2-0.3.1.7/Applications/xia2find.py ++++ b/xia2-0.3.1.7/Applications/xia2find.py +@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory + from Experts.FindImages import image2template_directory + + known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', +- 'osc', 'cbf', 'mar2000']] ++ 'osc', 'cbf', 'mar2000'] + known_sweeps = { } + + def is_image_name(file): +diff --git a/xia2-0.3.1.7/Experts/DRStrategyExpert.py b/xia2-0.3.1.7/Experts/DRStrategyExpert.py +index 28b1dc3..dba3ef7 100644 +--- a/xia2-0.3.1.7/Experts/DRStrategyExpert.py ++++ b/xia2-0.3.1.7/Experts/DRStrategyExpert.py +@@ -48,24 +48,24 @@ strategy_dict = { + 'default':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'default':{ + 'score':2, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} ++ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, + 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':2, + 'pipeline':{ +- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} ++ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, + 'depends-on':['xds', 'xscale']} + } +diff --git a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py +index 88f9218..5fb6f2a 100644 +--- a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py ++++ b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py +@@ -49,8 +49,8 @@ def Cad(DriverType = None): + self.add_command_line(hklin) + + self.set_task('Rewriting reflections %s => %s' % +- ` (os.path.split(hklin)[-1], +- ` os.path.split(self.getHklout())[-1])) ++ (os.path.split(hklin)[-1], ++ os.path.split(self.getHklout())[-1])) + + self.start() + diff --git a/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch new file mode 100644 index 000000000000..36cf6bb60d1d --- /dev/null +++ b/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch @@ -0,0 +1,61 @@ +diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py +index 1a3b0e2..e0b8a1e 100755 +--- a/xia2-0.3.3.1/Applications/xia2find.py ++++ b/xia2-0.3.3.1/Applications/xia2find.py +@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory + from Experts.FindImages import image2template_directory + + known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', +- 'osc', 'cbf', 'mar2000']] ++ 'osc', 'cbf', 'mar2000'] + known_sweeps = { } + + def is_image_name(file): +diff --git a/xia2-0.3.3.0/Experts/DRStrategyExpert.py b/xia2-0.3.3.0/Experts/DRStrategyExpert.py +index 28b1dc3..dba3ef7 100644 +--- a/xia2-0.3.3.1/Experts/DRStrategyExpert.py ++++ b/xia2-0.3.3.1/Experts/DRStrategyExpert.py +@@ -48,24 +48,24 @@ strategy_dict = { + 'default':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'default':{ + 'score':2, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} ++ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, + 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':2, + 'pipeline':{ +- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} ++ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, + 'depends-on':['xds', 'xscale']} + } +diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py +index 88f9218..5fb6f2a 100644 +--- a/xia2core-0.3.3.1/Python/Examples/CCP4/Cad.py ++++ b/xia2core-0.3.3.1/Python/Examples/CCP4/Cad.py +@@ -49,8 +49,8 @@ def Cad(DriverType = None): + self.add_command_line(hklin) + + self.set_task('Rewriting reflections %s => %s' % +- ` (os.path.split(hklin)[-1], +- ` os.path.split(self.getHklout())[-1])) ++ (os.path.split(hklin)[-1], ++ os.path.split(self.getHklout())[-1])) + + self.start() + diff --git a/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch new file mode 100644 index 000000000000..53cacbb5c681 --- /dev/null +++ b/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch @@ -0,0 +1,28 @@ +diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py +index 1a3b0e2..e0b8a1e 100755 +--- a/xia2-0.3.3.3/Applications/xia2find.py ++++ b/xia2-0.3.3.3/Applications/xia2find.py +@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory + from Experts.FindImages import image2template_directory + + known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', +- 'osc', 'cbf', 'mar2000']] ++ 'osc', 'cbf', 'mar2000'] + known_sweeps = { } + + def is_image_name(file): +diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py +index 88f9218..5fb6f2a 100644 +--- a/xia2core-0.3.3.3/Python/Examples/CCP4/Cad.py ++++ b/xia2core-0.3.3.3/Python/Examples/CCP4/Cad.py +@@ -49,8 +49,8 @@ def Cad(DriverType = None): + self.add_command_line(hklin) + + self.set_task('Rewriting reflections %s => %s' % +- ` (os.path.split(hklin)[-1], +- ` os.path.split(self.getHklout())[-1])) ++ (os.path.split(hklin)[-1], ++ os.path.split(self.getHklout())[-1])) + + self.start() + diff --git a/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch new file mode 100644 index 000000000000..9ba4c94495ea --- /dev/null +++ b/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch @@ -0,0 +1,28 @@ +diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py +index 1a3b0e2..e0b8a1e 100755 +--- a/xia2-0.3.4.0/Applications/xia2find.py ++++ b/xia2-0.3.4.0/Applications/xia2find.py +@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory + from Experts.FindImages import image2template_directory + + known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', +- 'osc', 'cbf', 'mar2000']] ++ 'osc', 'cbf', 'mar2000'] + known_sweeps = { } + + def is_image_name(file): +diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py +index 88f9218..5fb6f2a 100644 +--- a/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py ++++ b/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py +@@ -49,8 +49,8 @@ def Cad(DriverType = None): + self.add_command_line(hklin) + + self.set_task('Rewriting reflections %s => %s' % +- ` (os.path.split(hklin)[-1], +- ` os.path.split(self.getHklout())[-1])) ++ (os.path.split(hklin)[-1], ++ os.path.split(self.getHklout())[-1])) + + self.start() + diff --git a/sci-chemistry/xia2/metadata.xml b/sci-chemistry/xia2/metadata.xml new file mode 100644 index 000000000000..9ac9ffdb3a41 --- /dev/null +++ b/sci-chemistry/xia2/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/xia2/xia2-0.3.1.0.ebuild b/sci-chemistry/xia2/xia2-0.3.1.0.ebuild new file mode 100644 index 000000000000..33b3d841acfa --- /dev/null +++ b/sci-chemistry/xia2/xia2-0.3.1.0.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +inherit eutils python + +DESCRIPTION="An automated data reduction system for crystallography" +HOMEPAGE="http://www.ccp4.ac.uk/xia/" +SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + >=sci-chemistry/ccp4-apps-6.1.2 + sci-chemistry/mosflm + sci-chemistry/pointless + >=sci-libs/ccp4-libs-6.1.2 + sci-libs/cctbx" +DEPEND="${RDEPEND}" + +src_prepare() { + find . -name '*.bat' | xargs rm || die + + epatch "${FILESDIR}"/${PV}-fix-syntax.patch +} + +src_install() { + rm -rf ${P}/binaries ${PN}core-${PV}/Test || die + + insinto /usr/share/ccp4/XIAROOT/ + doins -r * || die + + # Set programs executable +# fperms cannot handle wildcards + chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die + chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die + + cat >> "${T}"/23XIA <<- EOF + XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT + XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV} + XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV} + PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications + EOF + + doenvd "${T}"/23XIA +} + +pkg_postinst() { + python_mod_optimize /usr/share/ccp4/XIAROOT +} + +pkg_postrm() { + python_mod_cleanup /usr/share/ccp4/XIAROOT +} diff --git a/sci-chemistry/xia2/xia2-0.3.1.6.ebuild b/sci-chemistry/xia2/xia2-0.3.1.6.ebuild new file mode 100644 index 000000000000..537735e1351f --- /dev/null +++ b/sci-chemistry/xia2/xia2-0.3.1.6.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +PYTHON_DEPEND="2" + +inherit eutils python + +DESCRIPTION="An automated data reduction system for crystallography" +HOMEPAGE="http://www.ccp4.ac.uk/xia/" +SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-chemistry/ccp4-apps-6.1.2 + sci-chemistry/mosflm + sci-chemistry/pointless + >=sci-libs/ccp4-libs-6.1.2 + sci-libs/cctbx" +DEPEND="${RDEPEND}" + +pkg_setup() { + python_set_active_version 2 +} + +src_prepare() { + find . -name '*.bat' -delete || die + + epatch "${FILESDIR}"/${PV}-fix-syntax.patch + python_convert_shebangs -r $(python_get_version) . +} + +src_install() { + rm -rf ${P}/binaries ${PN}core-${PV}/Test || die + + insinto /usr/share/ccp4/XIAROOT/ + doins -r * || die + + # Set programs executable +# fperms cannot handle wildcards + chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die + chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die + + cat >> "${T}"/23XIA <<- EOF + XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT + XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV} + XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV} + PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications + EOF + + doenvd "${T}"/23XIA +} + +pkg_postinst() { + python_mod_optimize /usr/share/ccp4/XIAROOT +} + +pkg_postrm() { + python_mod_cleanup /usr/share/ccp4/XIAROOT +} diff --git a/sci-chemistry/xia2/xia2-0.3.1.7.ebuild b/sci-chemistry/xia2/xia2-0.3.1.7.ebuild new file mode 100644 index 000000000000..16fbf797d1b4 --- /dev/null +++ b/sci-chemistry/xia2/xia2-0.3.1.7.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +PYTHON_DEPEND="2" + +inherit eutils python + +DESCRIPTION="An automated data reduction system for crystallography" +HOMEPAGE="http://www.ccp4.ac.uk/xia/" +SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-chemistry/ccp4-apps-6.1.2 + sci-chemistry/mosflm + sci-chemistry/pointless + >=sci-libs/ccp4-libs-6.1.2 + sci-libs/cctbx" +DEPEND="${RDEPEND}" + +pkg_setup() { + python_set_active_version 2 +} + +src_prepare() { + find . -name '*.bat' -delete || die + + epatch "${FILESDIR}"/${PV}-fix-syntax.patch + python_convert_shebangs -r $(python_get_version) . +} + +src_install() { + rm -rf ${P}/binaries ${PN}core-${PV}/Test || die + + insinto /usr/share/ccp4/XIAROOT/ + doins -r * || die + + # Set programs executable +# fperms cannot handle wildcards + chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die + chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die + + cat >> "${T}"/23XIA <<- EOF + XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT + XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV} + XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV} + PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications + EOF + + doenvd "${T}"/23XIA +} + +pkg_postinst() { + python_mod_optimize /usr/share/ccp4/XIAROOT +} + +pkg_postrm() { + python_mod_cleanup /usr/share/ccp4/XIAROOT +} diff --git a/sci-chemistry/xia2/xia2-0.3.3.1.ebuild b/sci-chemistry/xia2/xia2-0.3.3.1.ebuild new file mode 100644 index 000000000000..26fb7d0d4c83 --- /dev/null +++ b/sci-chemistry/xia2/xia2-0.3.3.1.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +PYTHON_DEPEND="2" + +inherit eutils python + +DESCRIPTION="An automated data reduction system for crystallography" +HOMEPAGE="http://www.ccp4.ac.uk/xia/" +SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-chemistry/ccp4-apps-6.1.2 + sci-chemistry/mosflm + sci-chemistry/pointless + >=sci-libs/ccp4-libs-6.1.2 + sci-libs/cctbx" +DEPEND="${RDEPEND}" + +pkg_setup() { + python_set_active_version 2 +} + +src_prepare() { + find . -name '*.bat' -delete || die + + epatch "${FILESDIR}"/${PV}-fix-syntax.patch + python_convert_shebangs -r $(python_get_version) . +} + +src_install() { + rm -rf ${P}/binaries ${PN}core-${PV}/Test || die + + insinto /usr/share/ccp4/XIAROOT/ + doins -r * || die + + # Set programs executable +# fperms cannot handle wildcards + chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die + chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die + + cat >> "${T}"/23XIA <<- EOF + XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT" + XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}" + XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}" + PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications" + EOF + + doenvd "${T}"/23XIA +} + +pkg_postinst() { + python_mod_optimize /usr/share/ccp4/XIAROOT + echo "" + elog "In order to use the package, you need to" + elog "\t source ${EPREFIX}/etc/profile" + echo "" +} + +pkg_postrm() { + python_mod_cleanup /usr/share/ccp4/XIAROOT +} diff --git a/sci-chemistry/xia2/xia2-0.3.3.3.ebuild b/sci-chemistry/xia2/xia2-0.3.3.3.ebuild new file mode 100644 index 000000000000..60778aa75fb9 --- /dev/null +++ b/sci-chemistry/xia2/xia2-0.3.3.3.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +PYTHON_DEPEND="2" + +inherit eutils python + +DESCRIPTION="An automated data reduction system for crystallography" +HOMEPAGE="http://www.ccp4.ac.uk/xia/" +SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-chemistry/ccp4-apps-6.1.2 + sci-chemistry/mosflm + sci-chemistry/pointless + >=sci-libs/ccp4-libs-6.1.2 + sci-libs/cctbx" +DEPEND="${RDEPEND}" + +pkg_setup() { + python_set_active_version 2 +} + +src_prepare() { + find . -name '*.bat' -delete || die + + epatch "${FILESDIR}"/${PV}-fix-syntax.patch + python_convert_shebangs -r $(python_get_version) . +} + +src_install() { + rm -rf ${P}/binaries ${PN}core-${PV}/Test || die + + insinto /usr/share/ccp4/XIAROOT/ + doins -r * || die + + # Set programs executable +# fperms cannot handle wildcards + chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die + chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die + + cat >> "${T}"/23XIA <<- EOF + XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT" + XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}" + XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}" + PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications" + EOF + + doenvd "${T}"/23XIA +} + +pkg_postinst() { + python_mod_optimize /usr/share/ccp4/XIAROOT + echo "" + elog "In order to use the package, you need to" + elog "\t source ${EPREFIX}/etc/profile" + echo "" +} + +pkg_postrm() { + python_mod_cleanup /usr/share/ccp4/XIAROOT +} diff --git a/sci-chemistry/xia2/xia2-0.3.4.0.ebuild b/sci-chemistry/xia2/xia2-0.3.4.0.ebuild new file mode 100644 index 000000000000..1d27abd355dc --- /dev/null +++ b/sci-chemistry/xia2/xia2-0.3.4.0.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +PYTHON_DEPEND="2" + +inherit eutils python + +DESCRIPTION="An automated data reduction system for crystallography" +HOMEPAGE="http://www.ccp4.ac.uk/xia/" +SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-chemistry/ccp4-apps-6.1.2 + sci-chemistry/mosflm + sci-chemistry/pointless + >=sci-libs/ccp4-libs-6.1.2 + sci-libs/cctbx" +DEPEND="${RDEPEND}" + +pkg_setup() { + python_set_active_version 2 +} + +src_prepare() { + find . -name '*.bat' -delete || die + + epatch "${FILESDIR}"/${PV}-fix-syntax.patch + python_convert_shebangs -r $(python_get_version) . +} + +src_install() { + rm -rf ${P}/binaries ${PN}core-${PV}/Test || die + + insinto /usr/share/ccp4/XIAROOT/ + doins -r * || die + + # Set programs executable +# fperms cannot handle wildcards + chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die + chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die + + cat >> "${T}"/23XIA <<- EOF + XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT" + XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}" + XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}" + PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications" + EOF + + doenvd "${T}"/23XIA +} + +pkg_postinst() { + python_mod_optimize /usr/share/ccp4/XIAROOT + echo "" + elog "In order to use the package, you need to" + elog "\t source ${EPREFIX}/etc/profile" + echo "" +} + +pkg_postrm() { + python_mod_cleanup /usr/share/ccp4/XIAROOT +} |