snaptron

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Bumps [numpy](https://github.com/numpy/numpy) from 1.9.3 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...

dependabot[bot]

pcat command not found inside docker container

3

The `deploy_docker.sh` script causes some errors as the `pcat` command is not found e.g.: >/deploy/srav3h/deploy//build_sqlite_db.sh: line 9: pcat: command not found The command is used in [deploy/build_sqlite_db.sh](https://github.com/ChristopherWilks/snaptron/commit/cee810ba68a74d7654dbb4f5ad15f9985d219142#diff-b8ee4cae59e61b232c73b110ae0fc8d59d9a779c4622dfa7d5eb67fdc2d5096e) > podman run...

klugem

The Snaptron docker image on quay.io currently doesn't work when pulled and converted to Singularity 2.8.0.

ChristopherWilks

Truncation of results in the presence of very large queries/high number of concurrent queries

3

Seen this on both Stingray and on the cluster mirror. Typically only happens when there are queries which return large numbers of rows (10000's) or the rows themselves are extremely...

ChristopherWilks

Inquire the intron junctions of srav2

1

Hi, I'm recently using snaptron for my analysis. I saw there is a column called "DataSource:Type" （https://snaptron.cs.jhu.edu/srav2/snaptron?regions=ABCD3）, but I could find it in the srav2-junction files (https://snaptron.cs.jhu.edu/data/srav2/junctions.bgz). Would please tell...

tewengtong

recount::snaptron_query() is broken on BioC 3.16 and 3.17

1

Hi, Currently all snaptron-related tests at `recount` are failing. That is, https://github.com/leekgroup/recount/blob/7301c5fc09c968110d50617eef43a635b03fd4a2/tests/testthat/test-data.R#L176-L201. Here's part of the output. ```R master* > snap snap_v2 snap_gtex snap_tcga expect_equal(length(snap), 3) Error: length(snap) not equal...

lcolladotor

Missing Files in Snaptron Server Startup

2

Hello, I have followed the singularity steps to get the encode1159 server running locally, as well as a custom snaptron db with data I processed via monorail. For setup of...

qhauck16