diff --git a/CHANGELOG.md b/CHANGELOG.md
index d5edd6e..99f0ff1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,8 @@
- save taxIds in `int32` instead of `uint32`, as BLAST and DIAMOND do. [#70](https://github.com/shenwei356/taxonkit/issues/70)
- `taxonkit list`:
- do not skip visited subtrees when some of give taxids are descendants of others. [#68](https://github.com/shenwei356/taxonkit/issues/68)
+ - `taxonkit`:
+ - When environment variable `TAXONKIT_DB` is set, explicitly setting --data-dir will overide the value of `TAXONKIT_DB`.
- [TaxonKit v0.13.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
[](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
- `taxonkit reformat`:
diff --git a/doc/docs/download.md b/doc/docs/download.md
index 2290656..781b184 100644
--- a/doc/docs/download.md
+++ b/doc/docs/download.md
@@ -6,18 +6,14 @@
## Current Version
-- [TaxonKit v0.13.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
-[](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
- - `taxonkit reformat`:
- - add a new placeholder `{K}` for rank `kingdom`. [#64](https://github.com/shenwei356/taxonkit/issues/64)
- - do not panic for invalid TaxIds, e.g., the column name, when using `-I--taxid-field`.
- - `taxonkit create-taxdump`:
- - fix merged.dmp and delnodes.dmp. Thanks to @apcamargo ! [gtdb-taxdump/issues/2](https://github.com/shenwei356/gtdb-taxdump/issues/2).
- - fix bug of handling non-GTDB data when using `-A/--field-accession` and no rank names given:
- the colname of the accession column would be treated as one of the ranks, which messed up all the ranks.
- - fix the default option value of `--field-accession-re` which wrongly remove prefix like `Sp_`. [#65](https://github.com/shenwei356/taxonkit/issues/65)
+- [TaxonKit v0.14.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.0)
+[](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.0)
+ - `taxonkit create-taxdump`:
+ - save taxIds in `int32` instead of `uint32`, as BLAST and DIAMOND do. [#70](https://github.com/shenwei356/taxonkit/issues/70)
- `taxonkit list`:
- - fix warning message of merged taxids.
+ - do not skip visited subtrees when some of give taxids are descendants of others. [#68](https://github.com/shenwei356/taxonkit/issues/68)
+ - `taxonkit`:
+ - When environment variable `TAXONKIT_DB` is set, explicitly setting --data-dir will overide the value of `TAXONKIT_DB`.
### Please cite
@@ -34,11 +30,11 @@
OS |Arch |File, 中国镜像 |Download Count
:------|:---------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/taxonkit_linux_amd64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_amd64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/taxonkit_linux_amd64.tar.gz)
-Linux |**arm64** |[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/taxonkit_linux_arm64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_arm64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/taxonkit_linux_arm64.tar.gz)
-macOS |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/taxonkit_darwin_amd64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_amd64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/taxonkit_darwin_amd64.tar.gz)
-macOS |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/taxonkit_darwin_arm64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_arm64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/taxonkit_darwin_arm64.tar.gz)
-Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/taxonkit_windows_amd64.exe.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_windows_amd64.exe.tar.gz)|[](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/taxonkit_windows_amd64.exe.tar.gz)
+Linux |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_linux_amd64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_amd64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_linux_amd64.tar.gz)
+Linux |**arm64** |[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_linux_arm64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_arm64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_linux_arm64.tar.gz)
+macOS |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_darwin_amd64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_amd64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_darwin_amd64.tar.gz)
+macOS |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_darwin_arm64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_arm64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_darwin_arm64.tar.gz)
+Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_windows_amd64.exe.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_windows_amd64.exe.tar.gz)|[](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_windows_amd64.exe.tar.gz)
## Installation
@@ -159,6 +155,18 @@ All-in-one command:
## Release history
+- [TaxonKit v0.13.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
+[](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
+ - `taxonkit reformat`:
+ - add a new placeholder `{K}` for rank `kingdom`. [#64](https://github.com/shenwei356/taxonkit/issues/64)
+ - do not panic for invalid TaxIds, e.g., the column name, when using `-I--taxid-field`.
+ - `taxonkit create-taxdump`:
+ - fix merged.dmp and delnodes.dmp. Thanks to @apcamargo ! [gtdb-taxdump/issues/2](https://github.com/shenwei356/gtdb-taxdump/issues/2).
+ - fix bug of handling non-GTDB data when using `-A/--field-accession` and no rank names given:
+ the colname of the accession column would be treated as one of the ranks, which messed up all the ranks.
+ - fix the default option value of `--field-accession-re` which wrongly remove prefix like `Sp_`. [#65](https://github.com/shenwei356/taxonkit/issues/65)
+ - `taxonkit list`:
+ - fix warning message of merged taxids.
- [TaxonKit v0.12.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.12.0)
[](https://github.com/shenwei356/taxonkit/releases/tag/v0.12.0)
- `taxonkit create-taxdump`:
diff --git a/doc/docs/usage.md b/doc/docs/usage.md
index 028b9fa..6c845c6 100644
--- a/doc/docs/usage.md
+++ b/doc/docs/usage.md
@@ -41,7 +41,7 @@ All-in-one command:
```text
TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit
-Version: 0.13.1
+Version: 0.14.0
Author: Wei Shen
@@ -59,6 +59,9 @@ Dataset:
or some other directory, and later you can refer to using flag --data-dir,
or environment variable TAXONKIT_DB
+
+ When environment variable TAXONKIT_DB is set, explicitly setting --data-dir will
+ overide the value of TAXONKIT_DB.
Usage:
taxonkit [command]
diff --git a/taxonkit/cmd/root.go b/taxonkit/cmd/root.go
index dfef744..636c1aa 100644
--- a/taxonkit/cmd/root.go
+++ b/taxonkit/cmd/root.go
@@ -73,7 +73,10 @@ Dataset:
"%s"
or some other directory, and later you can refer to using flag --data-dir,
- or environment variable TAXONKIT_DB
+ or environment variable TAXONKIT_DB.
+
+ When environment variable TAXONKIT_DB is set, explicitly setting --data-dir will
+ overide the value of TAXONKIT_DB.
`, VERSION, defaulDataDir)
diff --git a/taxonkit/cmd/util-cli.go b/taxonkit/cmd/util-cli.go
index 1990ac4..44ff1e1 100644
--- a/taxonkit/cmd/util-cli.go
+++ b/taxonkit/cmd/util-cli.go
@@ -64,7 +64,11 @@ func getConfigs(cmd *cobra.Command) Config {
var val, dataDir string
if val = os.Getenv("TAXONKIT_DB"); val != "" {
- dataDir = val
+ if cmd.Flags().Lookup("data-dir").Changed { // users explicitly set the option
+ dataDir = getFlagString(cmd, "data-dir")
+ } else {
+ dataDir = val
+ }
} else {
dataDir = getFlagString(cmd, "data-dir")
}