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Author SHA1 Message Date
Airistotal 664897e9c6 Added home.py to the flake test 
Fixed home.py to be compliant with flake tests
 2015-07-16 14:26:39 -05:00
Airistotal 923f7b085c Fixed UTC vs. CST time problems 
Fixed formatting issues for charts
 2015-07-16 14:15:15 -05:00
Airistotal c900528fe2 Moved css style to base.less 2015-07-16 11:45:56 -05:00
Airistotal 4d0243e715 Added home button to go back to the homepage 2015-07-16 11:41:58 -05:00
Airistotal dab8f42195 Added tool tips 
Changed titles to be more descriptive
 2015-07-15 15:27:06 -05:00
John Chilton 3deaf2f103 Merge pull request #389 from iracooke/dev 
Proteomics Datatypes
 2015-06-27 07:18:20 -05:00
Ira Cooke 484e2f72ca pep8 fixes 2015-06-27 08:47:26 +10:00
Ira Cooke 089cd474d0 Change raw to thermo.raw 2015-06-27 08:42:45 +10:00
John Chilton c65185d8bc Merge pull request #397 from guerler/workflow_form_002 
Strip former workflow editor, move js-files to sub-directory in mvc
 2015-06-26 12:11:01 -05:00
Ira Cooke a85d03ff0d Add back Binary.sniffable code because sniffing doesn't work properly without it 2015-06-26 12:23:55 +10:00
Ira Cooke cca245c62c Change RAW to ThermoRAW and add to sniffers 2015-06-26 06:24:18 +10:00
John Chilton 2ca436a5a4 Merge pull request #392 from galaxyproject/fix_bootstrap 
Fix getting admin key when bootstrapping toolshed.
 2015-06-25 11:29:09 -04:00
Dave B 97b19e422c Manually cherry-pick ecf8973484248c37f8dc96670f14a5ecce1a0c18. 2015-06-25 11:23:10 -04:00
John Chilton 2bb4d5f48b Merge pull request #399 from nsoranzo/dev 
[GCC2015] Fixes for ReadTheDocs API documentation.
 2015-06-25 10:53:01 -04:00
Nicola Soranzo 615dfb715b Extended the basic flake8 checks to (almost) all lib/ . 2015-06-25 12:45:46 +01:00
Nicola Soranzo d501396f70 PEP-8 and pylint fixes for lib/galaxy/model/search.py . 2015-06-25 12:45:46 +01:00
Nicola Soranzo 7556c9a2b2 Fix sphinx doc building of galaxy.webapps.galaxy.api.search . 2015-06-25 12:45:46 +01:00
Nicola Soranzo b29f724440 Almost complete PEP-8 fixes for api/tools.py . 2015-06-25 12:45:46 +01:00
Nicola Soranzo 8d2a6f2287 Fix sphinx doc building of galaxy.webapps.galaxy.api.tools . 2015-06-25 10:52:37 +01:00
Ira Cooke c2cf786e76 Remove trailing spaces on line 46 2015-06-25 09:06:42 +10:00
Ira Cooke 031b4e01c0 Back out trailing space removal 2015-06-25 09:06:02 +10:00
Ira Cooke fea0243eb2 Fix MsP sniffer 2015-06-25 08:59:12 +10:00
guerler 61024b832e Add missing packed files 2015-06-24 15:42:46 -04:00
guerler e51cd719dc Fix remaining qunit test cases for the workflow editor 2015-06-24 13:56:02 -04:00
guerler 53d13e9284 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 2015-06-24 12:58:53 -04:00
guerler 63fee8f7ce Undo merged fixed, replace underscore path rewrite 2015-06-24 12:33:17 -04:00
guerler 1ae11cbe08 Fix default qunit test cases for the workflow editor 2015-06-24 12:08:40 -04:00
Nicola Soranzo 416785e16d Update rst docs for bab978a4f4 . 2015-06-24 16:24:25 +01:00
John Chilton bfc0a22780 Merge pull request #384 from dctrud/parse_builds_fix 
Use passed in URL for getbuilds method of parse_builds.py
 2015-06-24 11:12:09 -04:00
David Trudgian 4e537c86e1 Merge pull request #1 from nsoranzo/for_dctrud 
Code cleanup. from @nsoranzo
 2015-06-24 10:09:00 -05:00
Eric Rasche f090fb80b0 Merge pull request #395 from jmchilton/tool_env_vars 
Allow environment variable definitions in tool XML.
 2015-06-24 09:16:53 -05:00
John Chilton 7879327c34 Add more interesting expression to environment_variables demo tool. 
Per suggestion by @nsoranzo (https://github.com/galaxyproject/galaxy/pull/395#issuecomment-114827531).
 2015-06-24 08:55:44 -04:00
John Chilton 78a69c09a3 Better file I/O handling for refactored code. 
Suggested by @nsoranzo (https://github.com/galaxyproject/galaxy/pull/395#discussion_r33136542).
 2015-06-24 08:45:33 -04:00
Nicola Soranzo 717b2064f4 Fix missing substitution from f98d4b27a0 . 2015-06-24 12:26:30 +01:00
Nicola Soranzo 9130734512 Simplify code. 2015-06-24 12:15:54 +01:00
Nicola Soranzo 56f9303fce PEP-8 fixes. 2015-06-24 12:12:27 +01:00
Nicola Soranzo 2299839981 Merge pull request #394 from jmchilton/tool_unit_test_pep 
PEP-8 fixes for entire test/unit/tools module.
 2015-06-24 11:34:00 +01:00
John Chilton 3784fece91 Allow environment variable definitions in tool XML. 
An ``<environment_variables>`` top-level XML block can be used to define these.

```
<environment_variables>
    <environment_variable name="FOO">$bar</environment_variable>
    <environment_variable name="FOO2">$bar2</environment_variable
</environment_variables>
```

The expressions are contained in the text of the block.

Implementation Detials:

In order to avoid odd shell expression stuff - the evaluated expressions are written to files and environment variables are read from these files at runtime.

Testing:

A demo tool ``test/functional/tools/environment_variables.xml`` with a test case that can be executed with the following expression.

```
./run_tests.sh -framework -id environment_variables
```
 2015-06-23 20:27:07 -04:00
John Chilton 8ac5eb98a5 PEP-8 fixes for entire test/unit/tools module. 
Add the module to .ci/pep8_sources.txt.
 2015-06-23 20:07:27 -04:00
Ira Cooke 98edbadf68 Syntax fixes 2015-06-24 09:54:30 +10:00
Ira Cooke aad8cb1902 pep8 fixes 2015-06-24 09:49:09 +10:00
Ira Cooke 990535a280 Include proteomics.py in pep8_sources 2015-06-24 09:16:46 +10:00
Ira Cooke 0e6fe6f279 Don't add proteomics.py to registry.py 2015-06-24 09:16:19 +10:00
Ira Cooke 1e86a77589 Add fixes suggested by John Chilton 2015-06-24 09:15:57 +10:00
Ira Cooke 3593d9c45c Remove trailing spaces 2015-06-24 09:10:14 +10:00
Dave B. 3eb203437c Fix getting admin key when bootstrapping toolshed. 2015-06-23 16:00:55 -04:00
Dannon Baker fcd5552bdd Merge pull request #386 from dannon/update_release_timeline 
Update 15.07 timeline to post-GCC
 2015-06-23 10:38:28 -04:00
Dannon Baker 952089e67b Merge branch 'master' into dev 2015-06-23 10:28:29 -04:00
Dannon Baker 9d609a466d Merge branch 'release_15.05' 2015-06-23 10:28:07 -04:00
Dannon Baker 9a3217e10a Merge pull request #390 from carlfeberhard/dev 
UI, History structure: fix/update serializer call to non-trans form
 2015-06-23 10:13:00 -04:00