Update sra-human-scrubber to 2.0.0

[BiocondaBot]

Update sra-human-scrubber: 1.0.2021_05_05 → 2.0.0

Info	Link or Description
Recipe	recipes/sra-human-scrubber (click to view/edit other files)
Summary	An SRA tool identifies and removes any significant human read, and outputs the edited (cleaned) fastq file for SRA submission.
Home	https://github.com/ncbi/sra-human-scrubber
Releases	https://github.com/ncbi/sra-human-scrubber/tags
Recipe Maintainer(s)	@rpetit3
Author	@ncbi

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This pull request was automatically generated (see docs).

[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
noarch	sra-human-scrubber-2.0.0-hdfd78af_0.tar.bz2	LinuxArtifacts

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You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c packages <package name>

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Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package	Tag	Install with docker
sra-human-scrubber	2.0.0--hdfd78af_0	show gzip -dc LinuxArtifacts/images/sra-human-scrubber:2.0.0--hdfd78af_0.tar.gz | docker load

[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
noarch	sra-human-scrubber-2.0.0-hdfd78af_0.tar.bz2	LinuxArtifacts

---

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c packages <package name>

---

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package	Tag	Install with docker
sra-human-scrubber	2.0.0--hdfd78af_0	show gzip -dc LinuxArtifacts/images/sra-human-scrubber:2.0.0--hdfd78af_0.tar.gz | docker load

[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
noarch	sra-human-scrubber-2.0.0-hdfd78af_0.tar.bz2	LinuxArtifacts

---

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c packages <package name>

---

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package	Tag	Install with docker
sra-human-scrubber	2.0.0--hdfd78af_0	show gzip -dc LinuxArtifacts/images/sra-human-scrubber:2.0.0--hdfd78af_0.tar.gz | docker load

[rpetit3]

Testing

Build DB

init_db.sh
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100    11  100    11    0     0     60      0 --:--:-- --:--:-- --:--:--    60
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  959M  100  959M    0     0  51.2M      0  0:00:18  0:00:18 --:--:-- 29.0M

Run Test

scrub.sh -t
2022-09-19 20:33:36     aligns_to version 0.707
2022-09-19 20:33:36     hardware threads: 32, omp threads: 32
2022-09-19 20:33:37     loading time (sec) 0
2022-09-19 20:33:37     /tmp/tmp.TYJxGLE01E/temp.fasta
2022-09-19 20:33:37     FastaReader
2022-09-19 20:33:37     100% processed
2022-09-19 20:33:37     total spot count: 2
2022-09-19 20:33:37     total read count: 2
2022-09-19 20:33:37     total time (sec) 0
1  spot(s) masked or removed.

test succeeded

Run with my own data

scrub.sh -i test.fq -o scrubbed.fq
2022-09-19 20:37:40     aligns_to version 0.707
2022-09-19 20:37:40     hardware threads: 32, omp threads: 32
2022-09-19 20:37:40     loading time (sec) 0
2022-09-19 20:37:40     /tmp/tmp.2JHCb7VNk7/temp.fasta
2022-09-19 20:37:40     FastaReader
2022-09-19 20:37:40     0% processed
2022-09-19 20:37:41     100% processed
2022-09-19 20:37:41     total spot count: 388060
2022-09-19 20:37:41     total read count: 388060
2022-09-19 20:37:41     total time (sec) 1
182  spot(s) masked or removed.

Think we are good to go

[rpetit3]

@BiocondaBot please merge

[BiocondaBot]

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.