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DownloadPageMain.DownloadPage HistoryHide minor edits - Show changes to markup May 16, 2007, at 01:24 PM
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Installation (web-based applications)
Asterias common has several files that can be used as examples. Most of the applications call "tryRrun.py" and it is likely that you will need to modify the paths. Likewise, the files in Asterias-common provide examples for monitoring applications, logging, etc. Paths here will probably need to be modified. You will also probably need to change the IPs of the hosts of your cluster.
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The code for the project is also mirrored at Launchpad. You can check there for alternative ways to download (and somewhat more verbose comments with maybe more detail). to:
The code for the project is also mirrored at Launchpad. You can check there for alternative ways to download (and somewhat more verbose comments with maybe more detail). May 04, 2007, at 11:11 AM
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All the code for ADaCGH. This includes the stand-alone ADaCGH R package. The best is for you to grab the complete sources: to:
All the code for ADaCGH. This includes the stand-alone ADaCGH R package. The best is for you to grab the complete sources: January 04, 2007, at 10:57 AM
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IDconverter and IDClightYou know what do do already :-). Please note that we use databases which are not included in the download (they are huge, and they are periodically updated).
January 03, 2007, at 01:02 PM
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This is a pre-alpha version of an attempt to make Asterias as easy to install as doing "easy_install asterias" (well, almost). But this is still pre-alpha (i.e., it does not really work). There are issues to solve both in the application code itself, and also figuring out a good way of having the paster server, asterias, and apache to get along well. You can get the code doing: to:
This is a pre-alpha version of an attempt to make Asterias as easy to install as doing "easy_install asterias" (well, almost). to clean up the code, to get rid of lots of code duplication, and to make the logic of the programs simpler. But this is still pre-alpha (i.e., it does not really work). There are issues to solve both in the application code itself, and also figuring out a good way of having the paster server, asterias, and apache to get along well. You can get the code doing: January 03, 2007, at 12:59 PM
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The code for the project is also mirrored at Launchpad. You can check there for alternative ways to download. to:
The code for the project is also mirrored at Launchpad. You can check there for alternative ways to download (and somewhat more verbose comments with maybe more detail). January 03, 2007, at 12:59 PM
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DNMADAll the code for DNMAD. Download it doing This differs from the rest of applications both in the language (Perl instead of Python) and some of the internal logic. January 03, 2007, at 12:57 PM
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Asterias-pylonsThis is a pre-alpha version of an attempt to make Asterias as easy to install as doing "easy_install asterias" (well, almost). But this is still pre-alpha (i.e., it does not really work). There are issues to solve both in the application code itself, and also figuring out a good way of having the paster server, asterias, and apache to get along well. You can get the code doing: January 03, 2007, at 12:40 PM
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The code for the project is also mirrored at Launchpad. to:
The code for the project is also mirrored at Launchpad. You can check there for alternative ways to download. Deleted line 63:
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TnasasAll the code for Tnasas. Download it doing December 29, 2006, at 09:41 AM
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SignSAll the code for SignS. Download it doing GeneSrFAll the code for GeneSrF. Download it doing Changed lines 111-114 from:
The rest of Asterias is not yet ready for download: we are refactoring a lot of code to make it simpler to install anywhere and it is taking longer than we thought. We will be releasing the different pieces as they become ready. to:
The rest will be available very soon. December 21, 2006, at 08:11 AM
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All the code for ADaCGH. This includes of the stand-alone ADaCGH R package. The best is for you to grab the complete sources: to:
All the code for ADaCGH. This includes the stand-alone ADaCGH R package. The best is for you to grab the complete sources: Changed lines 35-36 from:
(just in case: the version might have changed; visit the page and check it out and update if needed). to:
(the version might have changed; visit the page and check it out and update if needed). December 21, 2006, at 08:11 AM
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Pomelo IIAll the code for Pomelo II. The C++ can be compiled for stand-alone operation. Download it doing
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Asterias commonThere are some installation instructions common to all Asterias web applications, scripts that might help you with the installation, LAM/MPI controlling scripts, etc. You will need this (or something similar) for all your attempts to install the web-based applications until we can finally provide a working Pylons-based egg installer.
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ADaCGHAll the code for ADaCGH. This includes of the stand-alone ADaCGH R package. The best is for you to grab the complete sources: but if you only want the R package you can just do (just in case: the version might have changed; visit the page and check it out and update if needed). Pomelo IIAll the code for Pomelo II. The C++ can be compiled for stand-alone operation. Download it doing October 22, 2006, at 02:48 PM
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Please note that comprehensive testing of the Javascript and AJAX functionality for Pomelo II is not included here. Instead, that testing is carried out using Selenium. See the Pomelo Selenium tests page. These tests have been verified with Opera (8.54) under Windows and Linux, Firefox 1.5 (Windows and Linux), Konqueror 3.5 (Linux) and Internet Explorer 1.6 (only Windows). These tests do not run under Opera 9.0 or 9.02 (something strange in the way the JS is processed by Opera). September 20, 2006, at 06:22 PM
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Most of Asterias is not yet (2006-06-05) ready for download: we are refactoring a lot of code to make it simpler to install anywhere and it is taking longer than we thought. We will be releasing the different pieces as they become ready. to:
The rest of Asterias is not yet ready for download: we are refactoring a lot of code to make it simpler to install anywhere and it is taking longer than we thought. We will be releasing the different pieces as they become ready. September 12, 2006, at 06:28 PM
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Downloading the codeSeptember 12, 2006, at 06:27 PM
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Pomelo IIAll the code for Pomelo II. The C++ can be compiled for stand-alone operation. Download it doing Functional Testing:The Python and R code for functional and regression testing. You will need Funkload for it to work. If you want to use the email reporting facilities, you will need to provide a login, password, and set of email recipients in the file /PomeloII/test_chron.py. The most recent code is available doing Changed lines 73-87 from:
Functional Testing:The Python and R code for functional and regression testing. You will need Funkload for it to work. If you want to use the email reporting facilities, you will need to provide a login, password, and set of email recipients in the file /PomeloII/test_chron.py. The most recent code is available doing to:
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Functional Testing:The Python and R code for functional and regression testing. You will need Funkload for it to work. If you want to use the email reporting facilities, you will need to provide a login, password, and set of email recipients in the file /PomeloII/test_chron.py. The most recent code is available doing
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varSelRF:The R package is available from CRAN in the usual tar.gz and zip formats. The most recent code is available doing A paper that describes one of the methods implemented there is available from BMC Bioinformatics. Changed lines 42-43 from:
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A description of the method implemented in RJaCGH is available as a technical report. to:
A description of the method implemented in RJaCGH is available as a COBRA Preprint Series Article. August 24, 2006, at 12:28 PM
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The code for the project is also mirrored at Launchpad. August 24, 2006, at 12:21 PM
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A description of the method is available as a technical report. to:
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Latest newsAsterias is not yet (2006-06-05) ready for download: we are refactoring a lot of code to make it simpler to install anywhere and it is taking longer than we thought. We will be releasing the different pieces as they become ready. Requirements:to:
Downloading the codeWe use Bazaar-NG for version control (reasons why we choose Bazaar). You'll have to install Bazaar and then do RJaCGH:The R package is available from CRAN in the usual tar.gz and zip formats. The most recent code is available doing A description of the method is available as a technical report. Other applicationsMost of Asterias is not yet (2006-06-05) ready for download: we are refactoring a lot of code to make it simpler to install anywhere and it is taking longer than we thought. We will be releasing the different pieces as they become ready. Requirements for the web-based applications:Deleted lines 51-57:
Downloading the codeWe use Bazaar-NG for version control (reasons why we choose Bazaar). You'll have to install Bazaar and then do June 05, 2006, at 09:40 AM
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See the licenses page for details, and the first lines of each file \ to:
See the LicensesPage for details, and the first lines of each file \ June 05, 2006, at 09:37 AM
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Download pageLatest newsAsterias is not yet (2006-06-05) ready for download: we are refactoring a lot of code to make it simpler to install anywhere and it is taking longer than we thought. We will be releasing the different pieces as they become ready. Requirements:
Downloading the codeWe use Bazaar-NG for version control (reasons why we choose Bazaar). You'll have to install Bazaar and then do Licenses we use for the codeSee the licenses page for details, and the first lines of each file you are interested in, since we use either the GPL or the Affero GPL. |