Mercurial > repos > gga > chado_load_blast
annotate README.rst @ 8:0fccc2c639f5 draft
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 73142be24a0462a3aeb303401e8fcbc72f1cd4f5"
| author | gga |
|---|---|
| date | Mon, 14 Mar 2022 14:50:09 +0000 |
| parents | 1daff3b60f39 |
| children |
| rev | line source |
|---|---|
|
0
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
1 Galaxy-chado |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
2 ============= |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
3 |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
4 Galaxy tools to interface with Tripal using python-chado |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
5 |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
6 Dependencies |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
7 ------------ |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
8 |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
9 You will need to install some python modules in the Galaxy virtualenv for these |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
10 tools to be fully functional: |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
11 |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
12 .. code:: bash |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
13 |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
14 . /path/to/galaxy/.venv/bin/activate |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
15 pip install future chado |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
16 deactivate |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
17 |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
18 Environment |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
19 ----------- |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
20 |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
21 The following environment variables must be set: |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
22 |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
23 +--------------------------------+-----------------------------------------------------------+ |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
24 | ENV | Use | |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
25 +================================+===========================================================+ |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
26 | ``$GALAXY_CHADO_DBHOST`` | Host of the Chado database | |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
27 +--------------------------------+-----------------------------------------------------------+ |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
28 | ``$GALAXY_CHADO_DBNAME`` | Name of the Chado database | |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
29 +--------------------------------+-----------------------------------------------------------+ |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
30 | ``$GALAXY_CHADO_DBUSER`` | Username to connect to the database | |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
31 +--------------------------------+-----------------------------------------------------------+ |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
32 | ``$GALAXY_CHADO_DBPASS`` | Password to connect to the database | |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
33 +--------------------------------+-----------------------------------------------------------+ |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
34 | ``$GALAXY_CHADO_DBSCHEMA`` | Database schema. | |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
35 +--------------------------------+-----------------------------------------------------------+ |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
36 | ``$GALAXY_CHADO_DBPORT`` | Port of the Chado database | |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
37 +--------------------------------+-----------------------------------------------------------+ |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
38 |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
39 |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
40 License |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
41 ------- |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
42 |
|
1daff3b60f39
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff
changeset
|
43 All python scripts and wrappers are licensed under MIT license. |