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Dan Bolser dbolser-ebi

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dbolser-ebi / -
Created May 15, 2019 15:29
java version "1.7.0_201"
OpenJDK Runtime Environment (IcedTea 2.6.17) (7u211-2.6.17-0ubuntu0.1)
OpenJDK 64-Bit Server VM (build 24.201-b00, mixed mode)
@dbolser-ebi
dbolser-ebi / gist:cdb78cf3859fc68118efc87fa1e41ec4
Last active October 30, 2018 11:57
EXPLAIN SELECT COUNT(*) FROM tmp_sample_genotype_single_bp;
+----+-------------+-------+------+---------------+------+---------+------+------+------------------------------+
| id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |
+----+-------------+-------+------+---------------+------+---------+------+------+------------------------------+
| 1 | SIMPLE | NULL | NULL | NULL | NULL | NULL | NULL | NULL | Select tables optimized away |
+----+-------------+-------+------+---------------+------+---------+------+------+------------------------------+
1 row in set (0.00 sec)
EXPLAIN SELECT COUNT(DISTINCT variation_id) FROM tmp_sample_genotype_single_bp;
+----+-------------+-------------------------------+-------+---------------+---------------+---------+------+----------+--------------------------+
@dbolser-ebi
dbolser-ebi / -
Created October 17, 2018 09:53
2018-10-17 10:46:07,108 INFO - Retrieving results for job 117894
2018-10-17 10:46:07,135 INFO - Retrieving results for job 118472
2018-10-17 10:46:07,157 INFO - Retrieving results for job 139103
2018-10-17 10:46:07,181 INFO - Retrieving results for job 139991
2018-10-17 10:46:07,204 INFO - Retrieving results for job 140201
2018-10-17 10:46:07,251 INFO - Retrieving results for job 158129
2018-10-17 10:46:07,273 INFO - Retrieving results for job 158264
2018-10-17 10:46:07,296 INFO - Retrieving results for job 169452
2018-10-17 10:46:07,317 INFO - Retrieving results for job 170266
2018-10-17 10:46:07,339 INFO - Found tag one_off_test-20181017101930 for job: 171589
@dbolser-ebi
dbolser-ebi / build.checkoutDependencies.xml
Last active October 16, 2018 14:40
<?xml version="1.0"?>
<!--
Targets for checking out dependencies for the healthchecks.
Use
ant clean
to delete the directory with the checkouts.
@dbolser-ebi
dbolser-ebi / build.checkoutDependencies.xml
Created October 16, 2018 14:40
<?xml version="1.0"?>
<!--
Targets for checking out dependencies for the healthchecks.
Use
ant clean
to delete the directory with the checkouts.
@dbolser-ebi
dbolser-ebi / some.sql
Created October 15, 2018 11:03
SET @i=1;
SET @l=10000000;
SELECT * FROM seq_region INNER JOIN (SELECT @i, @i:=@i+@l AS x) AS der
ON length < @i
WHERE seq_region_id = 196420;
@dbolser-ebi
dbolser-ebi / dump_compara_orthologues.bash
Last active September 21, 2018 17:39
Generate Compara dumps for Plant Rectome (everything you need, I think)
## Get BioMart
git clone https://github.com/biomart/biomart-perl.git
## Get ready
cd biomart-perl/scripts
## Get Sharon's script from here:
@dbolser-ebi
dbolser-ebi / biomart_perl_query_4Justin.pl
Created September 21, 2018 09:50
Plant Reactome BioMart Perl API script for Justin
# An example script demonstrating the use of BioMart API.
# This perl API representation is only available for configuration versions >= 0.5
use strict;
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;
my $confFile = "../conf/martURLLocation.xml";
@dbolser-ebi
dbolser-ebi / bulk_hc.sh
Created August 7, 2018 08:47
source /homes/dbolser/EG_Places/Devel/lib/libensembl-94/setup.sh
release=41
# $ENSEMBL_ROOT_DIR/ensembl-production/scripts/process_division.sh \
# EPl mysql-pan-prod ensembl_production $release \
# > db_to_copy.txt
ENDPOINT=http://eg-prod-01.ebi.ac.uk:7000/hc/
@dbolser-ebi
dbolser-ebi / my.py
Last active November 28, 2017 10:49
from runstats import Statistics
stats = Statistics()
i=0
with open("dupes_default_run_scores.tsv") as tsv:
next(tsv)
for line in tsv:
i=i+1
line=line.rstrip()