Mercurial > repos > chrisb > gap_all_glycan_tools
comparison get_data/cfg/README_CFG.md @ 0:89592faa2875 draft
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| author | chrisb |
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| date | Wed, 23 Mar 2016 14:35:56 -0400 |
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| -1:000000000000 | 0:89592faa2875 |
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| 1 [TOC] | |
| 2 | |
| 3 # 1. cfg_get_glycan_from_cells.py | |
| 4 | |
| 5 Retrieve glycan profiling data from the CFG. | |
| 6 | |
| 7 With focus on retrieving the annotated mass spec data (.msa files) | |
| 8 | |
| 9 ## Works with Galaxy? | |
| 10 Yes. see [getcfgcells.xml](getcfgcells.xml) | |
| 11 | |
| 12 ## Command line usage | |
| 13 ``` | |
| 14 ../../virtualpy/bin/activate | |
| 15 python cfg_get_glycan_from_cells.py | |
| 16 ``` | |
| 17 | |
| 18 This will use the default settings and by default pull all data from the CFG. This may take some time. | |
| 19 The CFG may be unimpressed, if you do this too often. | |
| 20 | |
| 21 To specify which data you would like to retrieve : | |
| 22 ``` | |
| 23 ../../virtualpy/bin/activate | |
| 24 cfg_get_glycan_from_cells.py -s "$species" -p "$investigator" -g "$glycantype" -c "$celltype" -o "$html_file" --filepath "msa_output" | |
| 25 ``` | |
| 26 | |
| 27 ## Help | |
| 28 ``` | |
| 29 ../../virtualpy/bin/activate | |
| 30 python cfg_get_glycan_from_cells.py -h | |
| 31 ``` | |
| 32 | |
| 33 ## Unit Testing? | |
| 34 Not yet! Although some testing ha been done using the htmlfortesting.html and short-htmlfortesting.html. This code has also been used within Galaxy to retrieve data. | |
| 35 So it _should work just fine..._ | |
| 36 | |
| 37 In principle: | |
| 38 | |
| 39 ``` | |
| 40 ../../virtualpy/bin/activate | |
| 41 python test_cfg_get_glycan_from_cells.py | |
| 42 ``` |