source: extensions/net.sf.basedb.brcareg/trunk/README @ 1886

Last change on this file since 1886 was 1886, checked in by olle, 11 years ago

Fixed typo.

File size: 4.9 KB
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1== Requirements ==
2
3 1. BASE 3.2.1 or later.
4 
5== Introduction ==
6
7This package is an extension package to BASE that can be used to
8simplify biosource and sample registration.
9
10 * The homepage for this extension:
11   http://baseplugins.thep.lu.se/wiki/net.sf.basedb.brcareg
12
13== Installation and updating ==
14
15 1. Download the brcareg-*.tar.gz file.
16 2. Unpack the downloaded file to a directory of your choice.
17 3. Copy the 'brcareg.jar' file to your BASE plug-ins directory.
18    Eg. the directory specified by the 'plugins.dir' setting in 'base.config'.
19 4. Log in to BASE as a user with Administrator priviliges.
20 5. Go to 'Administrate->Plug-ins & Extensions->Overview' page.
21    Run the installation wizard and select to install/update 'brcareg.jar'.
22 6. Create a project and set it as the active project. This step is
23    optional but is recommended. Running BRCA-Reggie without an active project
24    will generate warning messages later on.
25 7. Go to the Extensions->BRCA-Reggie menu. Select the 'Installation wizard'
26    If the 'BRCA-Reggie' menu is not visible try BASE->Reload permissions menu.
27 8. It should display a list with several error message about missing items.
28    Click on the "Create missing items" button to create them.
29 9. Manual fixes. Check the release information if any manual changes are
30    needed to items that already exists in BASE.
3110. Done.
32
33== Using ==
34 
35BRCA-Reggie appears as a menu entry in the Extensions menu. All operations
36are available on that page.
37
38 * Installation wizard:
39   This entry is available if the logged in user is an 'Administrator' and
40   will perform some basic checks that items that are needed by BRCA-Reggie
41   exists and have been properly configured. Items that doesn't exists can
42   be created automatically.
43   
44 * Personal information registration wizard:
45   This entry is available for 'Administrators' and members of the
46   'PatientCurator' group. It is used to register new patients and
47   cases and connect this information to (already existing)
48   specimen tubes. It can also be used to update missing information
49   on existing cases and specimen tubes.
50 
51 * Blood referral form registration wizard
52   This entry is available for 'Administrators' and members of the
53   'PatientCurator' group. It is used to register blood samples
54   and connect them with patients. The patient doesn't have to exists.
55   If the blood sample already exists, the wizard can be used to update
56   missing information.
57
58 * Referral form registration wizard:
59   This entry is available for 'Administrators' and members of the
60   'PatientCurator' group. It is used to connect scanned referral
61   forms (eg. pdf files) to already existing cases.
62
63 * Consent form registration wizard:
64    This entry is available for 'Administrators' and members of the
65   'PatientCurator' group. It is used to connect register consent
66   for participating in the study.
67   
68 * Specimen tube registration wizard:
69   This entry is available for those with permission to create samples.
70   It is used to register new specimen tubes for cases that are not yet
71   in BASE.
72 
73 * Partition registration wizard:
74   This entry is available for those with permission to create samples
75   and extracts. It is used to register new partitions of existing
76   specimen tubes.
77   
78 * DNA/RNA extraction wizards
79   Wizards for registering the extraction of DNA and RNA from the
80   sample material.
81
82 * Histology wizards
83   Three wizards used in the process of creating H&E stained glass
84   slides. The first wizard creates a printable lab tracking protocol
85   for the current batch biomaterial items that are about to be
86   processed. The second wizard records the paraffin embedding step,
87   and the last wizard records the H&E staining step.
88
89 * RNA quality control wizards
90   Three wizards that are used in the RNA quality control workflow. The
91   first wizard is used for placing the RNA aliquots on a Caliper or
92   Bioanalyzer plate. The second wizard generates a sample name file that
93   can be used by the Caliper software. The third wizard import the results
94   from Caliper back into BASE.
95
96== Compiling ==
97
98To compile this package you also need:
99 
100 1. Ant 1.6
101 2. Java 1.6
102
103Follow these instructions:
104
105 1. Download the source code from the subversion repository. See
106    http://baseplugins.thep.lu.se/wiki/net.sf.basedb.brcareg for instructions.
107 
108 2. Type `ant download-lib` to automatically download the BASE core JAR files that
109    are neeed for compilation. You can also do this manually by copying the
110    base-*.jar files from the BASE installation directory
111    (<basedir>/www/WEB-INF/lib/) to the ./lib/compile directory.
112
113 3. Type 'ant' to compile the code and generate the 'brcareg.jar' file
114    in the project directory.
115
116 4. Use 'ant package' to create a downloadable tar.gz package.
117 
118Tip: If you need different values for any of the properties defined in
119the 'build.xml' file, create a file named 'build.properties' and set
120the values there.
121
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