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db7395b42378fe8aec00a5d25e452e033bc19164
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15 Commits
Author SHA1 Message Date
mvdbeek da1dd283f3 Add @TOOL_VERSION@ token for NCBI Datasets Genomes 2022-05-04 16:34:09 +02:00
mvdbeek 5c014d2048 Bump ncb-datasets-cli dependency to 13.14.0 
Fixes

```
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x10 pc=0x8a3fea]

goroutine 1 [running]:
main/datasets/datasets.downloadData(0xc000010380, 0x0, 0x0, 0x0, 0x7ffe36956316, 0x62, 0xffffffffffffffff, 0x0, 0x0)
	src/datasets/datasets/Download.go:41 +0xea
main/datasets/datasets.downloadAssembly(0xc000069100, 0x7ffe36956316, 0x62, 0x8ef4a0, 0xc000010298)
	src/datasets/datasets/DownloadGenome.go:63 +0x294
main/datasets/datasets.glob..func1(0xd9d080, 0xc000074730, 0x0, 0x5, 0x0, 0x0)
	src/datasets/datasets/Download.go:106 +0x2a7
github.com/spf13/cobra.(*Command).execute(0xd9d080, 0xc0000746e0, 0x5, 0x5, 0xd9d080, 0xc0000746e0)
	external/com_github_spf13_cobra/command.go:842 +0x472
github.com/spf13/cobra.(*Command).ExecuteC(0xd9cde0, 0x4686c5, 0xc000000180, 0x200000003)
	external/com_github_spf13_cobra/command.go:950 +0x375
github.com/spf13/cobra.(*Command).Execute(...)
	external/com_github_spf13_cobra/command.go:887
main/datasets/datasets.Execute()
	src/datasets/datasets/root.go:444 +0x31
main.main()
	src/cmd/datasets/main.go:10 +0x25
```
 2022-05-03 17:13:16 +02:00
Marius van den Beek 90c2f31cb4 Don't add ca-ceritificates to tool requirements 
ca-certificates is now part of the ncbi-datasets-cli conda package
 2021-11-18 17:17:19 +01:00
Marius van den BeekandHelena f1986a481f Export just once 
Thanks!

Co-authored-by: Helena <hxr@hx42.org>
 2021-11-17 15:28:07 +01:00
mvdbeek 47120ca48f Fix containerized NCBI Datasets Genomes data source tool 2021-11-12 20:17:34 +01:00
mvdbeek 63e25b20f4 Set profile version of ncbi_datasets so it can run containerized 2021-10-31 16:28:38 +01:00
mvdbeek a10645d664 Use ncbi_genome_dataset.zip format 2021-09-13 12:05:53 +02:00
mvdbeek 947832541b Use version_command tag, single quotes for paths 2021-09-09 19:15:19 +02:00
Brad Holmes 8b77edbb53 Implement NCBI Datasets Genome Dataset server 2021-09-09 12:28:02 -04:00
Brad Holmes 0186289a63 Improve wording and target URL for NCBI Datasets Genomes link tool 2021-09-08 11:00:39 -04:00
mvdbeek 44ee10e93d Add json_param as possible parameter type 2021-08-31 16:49:54 +02:00
mvdbeek 278b1422fd Replace taxon with generic file parameter 2021-08-31 16:45:56 +02:00
mvdbeek 58e530e65a Use separate dehydrated.zip datatype subclass 2021-08-31 16:45:56 +02:00
mvdbeek e552f79b49 Add dependency on ncbi-datasets-cli 2021-08-31 16:45:55 +02:00
mvdbeek e0855b7d9a Add simple NCBI datasets source tool 2021-08-31 16:45:55 +02:00