Source Code - Revision history

Randy: /* Repository */ Update to GitLab URL

2023-06-15T19:27:54Z

‎Repository: Update to GitLab URL

Rdo20 at 16:24, 3 October 2018

2018-10-03T16:24:08Z

Rdo20 at 23:33, 26 September 2018

2018-09-26T23:33:56Z

Rdo20 at 12:34, 26 April 2018

2018-04-26T12:34:42Z

Rdo20: /* Building Phaser from source */

2018-04-26T10:56:12Z

‎Building Phaser from source

Rdo20: /* Building Phaser from source */

2018-03-19T13:52:18Z

‎Building Phaser from source

Rdo20: /* Building Phaser from source */

2018-03-16T15:22:30Z

‎Building Phaser from source

Rdo20: /* Building Phaser from source */

2018-03-16T15:21:33Z

‎Building Phaser from source

Rdo20: /* Building Phaser from source */

2018-02-07T12:43:23Z

‎Building Phaser from source

Rdo20: /* Building Phaser from source */

2018-02-07T12:20:27Z

‎Building Phaser from source

@@ Line 1: / Line 1: @@
 ===Repository===
-A public [https://git.csx.cam.ac.uk/x/cimr-phaser/phaser.git/summary Phaser git repository] is available for '''git clone''' and '''git pull''' only. This mirrors commits to the Phaser SVN respository in real time
+A public [https://gitlab.developers.cam.ac.uk/scm/haematology/readgroup/phaser/-/tree/master/ Phaser GitLab repository] is available for '''git clone''' and '''git pull''' only. This mirrors commits to the Phaser SVN respository in real time
 The [http://www-structmed.cimr.cam.ac.uk/svn-cgi-bin/viewvc.cgi/ Phaser SVN repository] is located in Cambridge on the CIMR server (password restricted)

@@ Line 25: / Line 25: @@
 Phaser can be built as an executable file for the platforms Linux, MacOS, Windows (using VC++ 9.0) and Windows (using g++ in MinGW-W64). It can also be built as python modules useful for python scripting. There are two ways to achieve this.
+====Building from an existing CTBX Installation====
 The quick way is to start from an existing installation of CCTBX (available from http://cci.lbl.gov/cctbx_build/) to allow building the Phaser executable. Install CCTBX for the desired platform on your system first. For MinGW-W64 use the Windows build of CCTBX.
 Assuming python2.7 is present on your system Phaser can be built from a CCTBX installation
@@ Line 43: / Line 43: @@
 #On Linux or MacOS do '''libtbx.scons -j nproc exe/phaser''',  on Windows do '''libtbx.scons -j nproc exe\phaser.exe'''. Here nproc is the number of available CPUs to do the compilation. This will produce the Phaser executable within the build/exe directory. If Phaser python modules are also desired then omit the '''exe/phaser''' or '''exe\phaser.exe''' argument (does not apply to a MinGW-W64 build unless the installed version of your CCTBX was built for MinGW-W64).
+====Bootstrap build of Phaser====
 A simpler but slower way to build Phaser is to run a "bootstrap build". Download the file bootstrap.py (as detailed on https://github.com/cctbx/cctbx_project#installation ) to where you want to build phaser. Assuming that python 2.7 and the compiler is available from the PATH environment variable now run the command: <pre>python bootstrap.py --builder=phaser --nproc=8</pre> from a command prompt or bash shell. This will build a stripped down version of CCTBX in addition to Phaser and its python modules. The Phaser executable is located in the directory build/exe.

← Older revision		Revision as of 23:33, 26 September 2018
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	===Using Phaser from Python===		===Using Phaser from Python===
	Having compiled Phaser as above Phaser can now be accessed from the python interpreter that is part of CCTBX. To invoke it on Linux or MacOS it is necessary first to execute <pre>source build/setpaths.sh</pre> or on Windows <pre>build\setpaths.bat.</pre> From then on you can invoke python with the command <pre>cctbx.python</pre> and run scripts such as [[Python_Example_Scripts]]		Having compiled Phaser as above Phaser can now be accessed from the python interpreter that is part of CCTBX. To invoke it on Linux or MacOS it is necessary first to execute <pre>source build/setpaths.sh</pre> or on Windows <pre>build\setpaths.bat.</pre> From then on you can invoke python with the command <pre>cctbx.python</pre> and run scripts such as [[Python_Example_Scripts]]
		+
		+	===Nightly builds Regression Tests ===
		+	Regression tests of nightly builds are present on http://www-structmed.cimr.cam.ac.uk/Local/PhaserNightly/contents.html

← Older revision		Revision as of 12:34, 26 April 2018
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−	A simpler but slower way to build Phaser is to run a "bootstrap build". Download the file bootstrap.py (as detailed on https://github.com/cctbx/cctbx_project#installation ) to where you want to build phaser. Assuming that python 2.7 and the compiler is available from the PATH environment variable now run the command: <pre>python bootstrap.py --builder=phaser --nproc=8</pre> from a command prompt or bash shell. This will build a stripped down version of CCTBX in addition to Phaser and its python modules.	+	A simpler but slower way to build Phaser is to run a "bootstrap build". Download the file bootstrap.py (as detailed on https://github.com/cctbx/cctbx_project#installation ) to where you want to build phaser. Assuming that python 2.7 and the compiler is available from the PATH environment variable now run the command: <pre>python bootstrap.py --builder=phaser --nproc=8</pre> from a command prompt or bash shell. This will build a stripped down version of CCTBX in addition to Phaser and its python modules. The Phaser executable is located in the directory build/exe.


	The steps to build Phaser change from time to time as the developments of required components like CCTBX are moving targets. The steps outlined here may therefore differ from the actual ones at short or no notice.		The steps to build Phaser change from time to time as the developments of required components like CCTBX are moving targets. The steps outlined here may therefore differ from the actual ones at short or no notice.
		+
		+	===Using Phaser from Python===
		+	Having compiled Phaser as above Phaser can now be accessed from the python interpreter that is part of CCTBX. To invoke it on Linux or MacOS it is necessary first to execute <pre>source build/setpaths.sh</pre> or on Windows <pre>build\setpaths.bat.</pre> From then on you can invoke python with the command <pre>cctbx.python</pre> and run scripts such as [[Python_Example_Scripts]]

← Older revision		Revision as of 10:56, 26 April 2018
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−	A simpler but slower way to build Phaser is to run a "bootstrap build". Download the file bootstrap.py (as detailed on https://github.com/cctbx/cctbx_project#installation ) to where you want to build phaser. ~~Then~~ from ~~a command prompt~~ run the command: <pre>python bootstrap.py --builder=phaser --nproc=8.</pre> This will build a stripped down version of CCTBX in addition to Phaser and its python modules.	+	A simpler but slower way to build Phaser is to run a "bootstrap build". Download the file bootstrap.py (as detailed on https://github.com/cctbx/cctbx_project#installation ) to where you want to build phaser. Assuming that python 2.7 and the compiler is available from the PATH environment variable now run the command: <pre>python bootstrap.py --builder=phaser --nproc=8</pre> from a command prompt or bash shell. This will build a stripped down version of CCTBX in addition to Phaser and its python modules.


	The steps to build Phaser change from time to time as the developments of required components like CCTBX are moving targets. The steps outlined here may therefore differ from the actual ones at short or no notice.		The steps to build Phaser change from time to time as the developments of required components like CCTBX are moving targets. The steps outlined here may therefore differ from the actual ones at short or no notice.

@@ Line 26: / Line 26: @@
-One way is to start from an existing installation of CCTBX (available from http://cci.lbl.gov/cctbx_build/) to allow building the Phaser executable. Install CCTBX for the desired platform on your system first. For MinGW-W64 use the Windows build of CCTBX.
+The quick way is to start from an existing installation of CCTBX (available from http://cci.lbl.gov/cctbx_build/) to allow building the Phaser executable. Install CCTBX for the desired platform on your system first. For MinGW-W64 use the Windows build of CCTBX.
 Assuming python2.7 is present on your system Phaser can be built from a CCTBX installation
 with the following steps from a Bash shell or a Windows command prompt:
@@ Line 44: / Line 44: @@
-Another way to build Phaser is to run a "bootstrap build". Download the file bootstrap.py (as detailed on https://github.com/cctbx/cctbx_project#installation ) to where you want to build phaser. Then from a command prompt run the command: <pre>python bootstrap.py --builder=phaser --nproc=8.</pre> This will build a stripped down version of CCTBX in addition to Phaser and its python modules.
+A simpler but slower way to build Phaser is to run a "bootstrap build". Download the file bootstrap.py (as detailed on https://github.com/cctbx/cctbx_project#installation ) to where you want to build phaser. Then from a command prompt run the command: <pre>python bootstrap.py --builder=phaser --nproc=8.</pre> This will build a stripped down version of CCTBX in addition to Phaser and its python modules.
 The steps to build Phaser change from time to time as the developments of required components like CCTBX are moving targets. The steps outlined here may therefore differ from the actual ones at short or no notice.

@@ Line 31: / Line 31: @@
 #Edit '''config_modules.sh''' or '''config_modules.cmd''' script to like:
 #:*'''Linux or MacOS''':
-#:<pre>#!/bin/sh 1&#10;python ../modules/cctbx_project/libtbx/configure.py phaser --enable_openmp_if_possible=True</pre>
+#:<pre>#!/bin/sh &#10;python ../modules/cctbx_project/libtbx/configure.py phaser --enable_openmp_if_possible=True</pre>
 #:*'''Windows using Microsoft VC++ 9.0'''
 #:<pre>python ..\modules\cctbx_project\libtbx\configure.py phaser --enable_openmp_if_possible=True</pre>

@@ Line 26: / Line 26: @@
 Assuming python2.7 is present on your system Phaser can be built from a CCTBX installation
 with the following steps from a Bash shell or a Windows command prompt:
-*Change directory to the modules/ folder within the CCTBX installation. Then do
+#Change directory to the modules/ folder within the CCTBX installation. Then do <pre>git clone git://git.uis.cam.ac.uk/cimr-phaser/phaser.git </pre>
- git clone git://git.uis.cam.ac.uk/cimr-phaser/phaser.git
+#Change directory to the build/ folder within the CCTBX installation
-*Change directory to the build/ folder within the CCTBX installation
+#Delete all files and folders except '''config_modules.sh''' or '''config_modules.cmd'''
-*Delete all files and folders except '''config_modules.sh''' or '''config_modules.cmd'''
+#Edit '''config_modules.sh''' or '''config_modules.cmd''' script to like:
-*Edit '''config_modules.sh''' or '''config_modules.cmd''' script to like:
+#:*'''Linux or MacOS''':
-**'''Linux or MacOS''':
+#:<pre>#!/bin/sh 1&#10;python ../modules/cctbx_project/libtbx/configure.py phaser --enable_openmp_if_possible=True</pre>
- #!/bin/sh
+#:*'''Windows using Microsoft VC++ 9.0'''
- python ../modules/cctbx_project/libtbx/configure.py phaser --enable_openmp_if_possible=True
+#:<pre>python ..\modules\cctbx_project\libtbx\configure.py phaser --enable_openmp_if_possible=True</pre>
-:*'''Windows using Microsoft VC++ 9.0'''
+#:*'''Windows using MinGW-W64 5.3.0'''
- python ..\modules\cctbx_project\libtbx\configure.py phaser --enable_openmp_if_possible=True
+#:<pre>python ..\modules\cctbx_project\libtbx\configure.py phaser --enable_openmp_if_possible=True --compiler=mingw --static_exe</pre>
-:*'''Windows using MinGW-W64 5.3.0'''
+#Execute the '''config_modules.sh''' or '''config_modules.cmd''' script.
- python ..\modules\cctbx_project\libtbx\configure.py phaser --enable_openmp_if_possible=True --compiler=mingw --static_exe
+#On Linux or MacOS source the file '''setpaths.sh''', on Windows execute the file '''setpaths.bat'''
+#On Linux or MacOS do '''libtbx.scons -j nproc exe/phaser''',  on Windows do '''libtbx.scons -j nproc exe\phaser.exe'''. Here nproc is the number of available CPUs to do the compilation. This will produce the Phaser executable within the build/exe directory. If Phaser python modules are also desired then omit the '''exe/phaser''' or '''exe\phaser.exe''' argument (does not apply to a MinGW-W64 build unless the installed version of your CCTBX was built for MinGW-W64).
 The steps to build Phaser change from time to time as the developments of required components like CCTBX are moving targets. The steps outlined here may therefore differ from the actual ones at short or no notice.