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We need a smaller assembly from NCBI for testing #24

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bmpvieira opened this issue Apr 14, 2017 · 3 comments
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We need a smaller assembly from NCBI for testing #24

bmpvieira opened this issue Apr 14, 2017 · 3 comments
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@bmpvieira
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@bmpvieira bmpvieira commented Apr 14, 2017

Guillardia theta assembly file is around 50mb. This wasn't a problem when the tests were downloading it every time from NCBI. However, now we are mocking NCBI api with a cached version of the file (so that tests don't break every week due to NCBI side changes). So this file is now stored in git-lfs, and with TravisCI testing we quickly reach the 1GB/month free GitHub git-lfs bandwidth. Maybe there's a small virus, bacteria or DNA region on NCBI with a much smaller assembly.

@bmpvieira bmpvieira added the test label Apr 14, 2017
@tiagofilipe12
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@tiagofilipe12 tiagofilipe12 commented Apr 14, 2017

For instance: bionode-ncbi download assembly Stenotrophomonas acidaminiphila

@bmpvieira bmpvieira added this to Backlog in Bionode Project Board Apr 14, 2017
@tiagofilipe12 tiagofilipe12 self-assigned this Apr 14, 2017
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@tiagofilipe12 tiagofilipe12 commented Apr 14, 2017

Even better: Stenotrophomonas ginsengisoli unique assembly has 966.23 kB.

@bmpvieira bmpvieira moved this from Backlog to In Progress in Bionode Project Board Apr 14, 2017
@bmpvieira bmpvieira added this to the 1.8.0 milestone Apr 14, 2017
bmpvieira added a commit that referenced this issue Apr 14, 2017
We will enable them later once #24 is closed
This was referenced Apr 15, 2017
@tiagofilipe12
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@tiagofilipe12 tiagofilipe12 commented Apr 15, 2017

I actually found a more decent assembly from a small bacteria (Carsonella ruddii).

@bmpvieira bmpvieira changed the title We need a smaller SRA from NCBI for testing We need a smaller assembly from NCBI for testing Apr 15, 2017
tiagofilipe12 added a commit that referenced this issue Apr 15, 2017
Add smaller download assembly for testing and fix #24
tiagofilipe12 added a commit that referenced this issue Apr 15, 2017
@bmpvieira bmpvieira moved this from In Progress to Done in Bionode Project Board Apr 15, 2017
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