From a2e7589f7f48099e1fbb50c4451badb1f47aa4aa Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Sun, 27 Nov 2022 21:47:10 +0800 Subject: [PATCH] v0.14.0 --- CHANGELOG.md | 2 ++ doc/docs/download.md | 40 ++++++++++++++++++++++++---------------- doc/docs/usage.md | 5 ++++- taxonkit/cmd/root.go | 5 ++++- taxonkit/cmd/util-cli.go | 6 +++++- 5 files changed, 39 insertions(+), 19 deletions(-) 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) [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.13.0/total.svg)](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) -[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.13.0/total.svg)](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) +[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.14.0/total.svg)](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) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_amd64.tar.gz.svg?maxAge=3600)](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) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_arm64.tar.gz.svg?maxAge=3600)](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) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_amd64.tar.gz.svg?maxAge=3600)](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) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_arm64.tar.gz.svg?maxAge=3600)](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)|[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_windows_amd64.exe.tar.gz.svg?maxAge=3600)](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) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_amd64.tar.gz.svg?maxAge=3600)](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) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_arm64.tar.gz.svg?maxAge=3600)](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) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_amd64.tar.gz.svg?maxAge=3600)](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) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_arm64.tar.gz.svg?maxAge=3600)](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)|[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_windows_amd64.exe.tar.gz.svg?maxAge=3600)](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) +[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.13.0/total.svg)](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) [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.12.0/total.svg)](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") }