source: extensions/net.sf.basedb.reggie/trunk/README

Last change on this file was 6326, checked in by Nicklas Nordborg, 7 months ago

Merge Reggie 4.31.3 to the trunk

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[1282]1== Requirements ==
2
[6183]3 1. BASE 3.18.1
[6326]4 2. Open Grid Scheduler extension 1.4 must be installed
[6052]5 3. Thumbnails extension 1.2 must be installed
[1282]6 
7== Introduction ==
8
9This package is an extension package to BASE that can be used to
10simplify biosource and sample registration.
11
12 * The homepage for this extension:
[6309]13   https://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie
[1282]14
[1463]15== Installation and updating ==
[1282]16
17 1. Download the reggie-*.tar.gz file.
18 2. Unpack the downloaded file to a directory of your choice.
[1463]19 3. Copy the 'reggie.jar' file to your BASE plug-ins directory.
20    Eg. the directory specified by the 'plugins.dir' setting in 'base.config'.
[2747]21 4. Edit and copy configuration files to their correct location. See
22    config/readme.txt for more information. If this is a first-time
23    installation shut down BASE and run 'updatedb.sh' script so
24    that additional reporter annotations and raw data columns are
25    created.
26 5. Log in to BASE as a user with Administrator priviliges.
27 6. Go to 'Administrate->Plug-ins & Extensions->Overview' page.
[1463]28    Run the installation wizard and select to install/update 'reggie.jar'.
[2747]29 7. Create a project and set it as the active project. This step is
[1310]30    optional but is recommended. Running Reggie without an active project
31    will generate warning messages later on.
[2747]32 8. Go to the Extensions->Reggie menu. Select the 'Installation wizard'
[1334]33    If the 'Reggie' menu is not visible try BASE->Reload permissions menu.
[2747]34 9. It should display a list with several error message about missing items.
[1310]35    Click on the "Create missing items" button to create them. If no project
36    was created in step 6, all annotatation types will be shared with the
37    'PatientCurator' group, otherwise only some will be shared to the
38    group and some will be shared to the active project.
[2747]3910. Manual fixes. Check the release information if any manual changes are
[1630]40    needed to items that already exists in BASE.
[2747]4111. Done.
[1301]42
43== Using ==
44 
[1282]45Reggie appears as a menu entry in the Extensions menu. All operations
[1301]46are available on that page.
[1282]47
[1334]48 * Installation wizard:
[1301]49   This entry is available if the logged in user is an 'Administrator' and
50   will perform some basic checks that items that are needed by Reggie
51   exists and have been properly configured. Items that doesn't exists can
52   be created automatically.
53   
[1334]54 * Personal information registration wizard:
[1301]55   This entry is available for 'Administrators' and members of the
56   'PatientCurator' group. It is used to register new patients and
57   cases and connect this information to (already existing)
[1334]58   specimen tubes. It can also be used to update missing information
59   on existing cases and specimen tubes.
[1527]60 
61 * Blood referral form registration wizard
62   This entry is available for 'Administrators' and members of the
63   'PatientCurator' group. It is used to register blood samples
64   and connect them with patients. The patient doesn't have to exists.
65   If the blood sample already exists, the wizard can be used to update
66   missing information.
67
[1337]68 * Referral form registration wizard:
69   This entry is available for 'Administrators' and members of the
70   'PatientCurator' group. It is used to connect scanned referral
71   forms (eg. pdf files) to already existing cases.
[1301]72
[1355]73 * Consent form registration wizard:
74    This entry is available for 'Administrators' and members of the
75   'PatientCurator' group. It is used to connect register consent
[1461]76   for participating in the study.
77   
78 * Specimen tube registration wizard:
79   This entry is available for those with permission to create samples.
80   It is used to register new specimen tubes for cases that are not yet
81   in BASE.
82 
83 * Partition registration wizard:
84   This entry is available for those with permission to create samples
85   and extracts. It is used to register new partitions of existing
86   specimen tubes.
[1645]87   
88 * DNA/RNA extraction wizards
89   Wizards for registering the extraction of DNA and RNA from the
90   sample material.
[1301]91
[1606]92 * Histology wizards
[1779]93   Three wizards used in the process of creating H&E stained glass
94   slides. The first wizard creates a printable lab tracking protocol
95   for the current batch biomaterial items that are about to be
96   processed. The second wizard records the paraffin embedding step,
97   and the last wizard records the H&E staining step.
[1606]98
[1557]99 * RNA quality control wizards
100   Three wizards that are used in the RNA quality control workflow. The
101   first wizard is used for placing the RNA aliquots on a Caliper or
102   Bioanalyzer plate. The second wizard generates a sample name file that
103   can be used by the Caliper software. The third wizard import the results
104   from Caliper back into BASE.
105
[1282]106== Compiling ==
107
[5443]108To compile this package you also need (later versions may also work):
[1282]109 
[5443]110 1. Ant 1.10
111 2. Java 11
[1282]112
113Follow these instructions:
114
115 1. Download the source code from the subversion repository. See
[6309]116    https://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie for instructions.
[1282]117 
118 2. Type `ant download-lib` to automatically download the BASE core JAR files that
119    are neeed for compilation. You can also do this manually by copying the
[1463]120    base-*.jar files from the BASE installation directory
121    (<basedir>/www/WEB-INF/lib/) to the ./lib/compile directory.
[1282]122
123 3. Type 'ant' to compile the code and generate the 'reggie.jar' file
124    in the project directory.
125
126 4. Use 'ant package' to create a downloadable tar.gz package.
127 
128Tip: If you need different values for any of the properties defined in
129the 'build.xml' file, create a file named 'build.properties' and set
130the values there.
131
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