Commit 2cdb8537 authored by Michael Baudis's avatar Michael Baudis
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Moved housekeeping commends to Readme

parent 43564786
......@@ -3,3 +3,13 @@ Beacon queries and interface for the MongoDB based _arrayMap_ cancer genome repo
Queries are contained inside the directory [mongo-queries](mongo-queries)
An alternative would be to transform the native _arrayMap_ data format into VCF, and to use [the Python Simple Beacon Server](https://github.com/maximilianh/ucscBeacon).
#### Download commands
The following command can be used to download a chunk of the _arrayMap_ dataset, e.g. to understand data structures.
```wget "http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&api_doctype=jsondata&randno=200" -O 200samples.json```
The next command would replace the current local _arrayMap_ instance with the downloaded file.
```mongoimport --drop --db arraymap --collection samples < 200samples.json --batchSize 1```
wget "http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&api_doctype=jsondata" -O 20Ksamples.json
## a smaller dataset
##wget "http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&withfollowup=y&api_doctype=jsondata" -O 89.json
mongoimport --drop --db arraymap --collection samples < 20Ksamples.json --batchSize 1
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