From 7cb3bf83a1c82d7904abd33494bf25707ad4ca93 Mon Sep 17 00:00:00 2001 From: victor5lm Date: Wed, 11 Sep 2024 15:45:03 +0200 Subject: [PATCH 1/8] Updated setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index dcda6436a..efa93a594 100755 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages -version = "2.1.0" +version = "2.2.0" with open("README.md") as f: readme = f.read() From 1aa39ba33366ccd4750a91730ef983d2f742006d Mon Sep 17 00:00:00 2001 From: victor5lm Date: Wed, 11 Sep 2024 15:48:29 +0200 Subject: [PATCH 2/8] Updated version tag in __main__.py --- bu_isciii/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bu_isciii/__main__.py b/bu_isciii/__main__.py index 16e99303d..3933a0272 100755 --- a/bu_isciii/__main__.py +++ b/bu_isciii/__main__.py @@ -57,7 +57,7 @@ def run_bu_isciii(): ) # stderr.print("[green] `._,._,'\n", highlight=False) - __version__ = "2.1.0" + __version__ = "2.2.0" stderr.print( "[grey39] BU-ISCIII-tools version {}".format(__version__), highlight=False ) From b581b6c925d26346a10d9f5e5006ce29f1d410cf Mon Sep 17 00:00:00 2001 From: victor5lm Date: Wed, 11 Sep 2024 15:50:26 +0200 Subject: [PATCH 3/8] Fixed a minor mistake in bioinfo_doc.py --- bu_isciii/bioinfo_doc.py | 1 + 1 file changed, 1 insertion(+) diff --git a/bu_isciii/bioinfo_doc.py b/bu_isciii/bioinfo_doc.py index 7852c423c..4da846728 100755 --- a/bu_isciii/bioinfo_doc.py +++ b/bu_isciii/bioinfo_doc.py @@ -187,6 +187,7 @@ def __init__( self.samples = self.resolution_info.get("samples", None) self.versions = self.load_versions() self.handled_services = None + self.all_services = None try: self.config_pdfkit = pdfkit.configuration() except OSError as e: From d7c7b24737050179ea2947d2cf0bf9a1370544d7 Mon Sep 17 00:00:00 2001 From: victor5lm Date: Wed, 11 Sep 2024 15:55:12 +0200 Subject: [PATCH 4/8] Updated the remove_columns_mapping_table.sh script --- .../viralrecon/ANALYSIS/remove_columns_mapping_table.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bu_isciii/templates/viralrecon/ANALYSIS/remove_columns_mapping_table.sh b/bu_isciii/templates/viralrecon/ANALYSIS/remove_columns_mapping_table.sh index 06f79c7f6..434c51c92 100644 --- a/bu_isciii/templates/viralrecon/ANALYSIS/remove_columns_mapping_table.sh +++ b/bu_isciii/templates/viralrecon/ANALYSIS/remove_columns_mapping_table.sh @@ -3,7 +3,8 @@ output_file=$(echo processed_mapping_illumina_$(date '+%Y%m%d').tab) # Removal of the first three columns of the mapping illumina tab file -cut --complement -f1-3 *.tab > output_file +cut --complement -f1-3 mapping_*.tab > output_file +mv $output_file mapping_illumina_$(date '+%Y%m%d').tab # Success message if [ $? -eq 0 ]; then From 5c788cb76f891c6006263f228bce319b235199bb Mon Sep 17 00:00:00 2001 From: victor5lm Date: Wed, 11 Sep 2024 15:55:47 +0200 Subject: [PATCH 5/8] Updated README.md --- README.md | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/README.md b/README.md index fa4f2e68f..da5522a9f 100644 --- a/README.md +++ b/README.md @@ -21,6 +21,7 @@ BU-ISCIII provides a serie or services in its portfolio for supporting bioinform - [bioinfo\_doc](#bioinfo_doc) - [archive](#archive) - [autoclean\_sftp](#autoclean_sftp) + - [fix-permissions](#fix-permissions) - [Acknowledgements](#acknowledgements) ## Installation @@ -94,6 +95,8 @@ Commands: finish Service cleaning, remove big files, rename folders before... bioinfo-doc Create the folder documentation structure in bioinfo_doc... archive Archive services or retrieve services from archive + autoclean-sftp Clean old sftp services + fix-permissions Fix permissions ``` #### list @@ -389,6 +392,26 @@ Options: --help Show this message and exit. ``` +#### fix-permissions + +Example of usage: + +```bash +bu-isciii fix-permissions -d /data/bi +``` + +Help: + +```bash +Usage: bu-isciii fix-permissions [OPTIONS] + + Fix permissions + +Options: + -d, --input_directory PATH Input directory to fix permissions (absolute path) [required] + --help Show this message and exit. +``` + ## Acknowledgements Python package idea and design is really inspired in [nf-core/tools](https://github.com/nf-core/tools). From 60b6c774ab1fe5ed475c7ff3d2b82cf42f6aa9d4 Mon Sep 17 00:00:00 2001 From: victor5lm Date: Wed, 11 Sep 2024 15:56:00 +0200 Subject: [PATCH 6/8] Updated CHANGELOG.md --- CHANGELOG.md | 42 +++++++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8313ac697..248b943c4 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,27 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [2.2.Xdev] - 2024-0X-XX : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.X +## [2.X.Xdev] - 2024-0X-XX : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.X + +### Credits + +Code contributions to the new version: + +### Template fixes and updates + +### Modules + +#### Added enhancements + +#### Fixes + +#### Changed + +#### Removed + +### Requirements + +## [2.2.0] - 2024-09-12 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.0 ### Credits @@ -96,26 +116,6 @@ Code contributions to the new version: ### Requirements -## [2.X.1hot] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.1 - -### Credits - -Code contributions to the hotfix: - -### Template fixes and updates - -### Modules - -#### Added enhancements - -#### Fixes - -#### Changed - -#### Removed - -### Requirements - ## [2.1.0] - 2024-04-19 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.1.0 ### Credits From 61f43a483327c5a76c8facc6fafed56c2eeb7f6f Mon Sep 17 00:00:00 2001 From: victor5lm Date: Thu, 12 Sep 2024 09:55:24 +0200 Subject: [PATCH 7/8] Updated CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 248b943c4..c2f9777fa 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -90,6 +90,7 @@ Code contributions to the new version: - Updated several templates (singularity images, outdated paths, improvements, etc) [#331](https://github.com/BU-ISCIII/buisciii-tools/pull/331) - Added permissions fixing after running scratch_copy, as well as a new fix-permissions module in the tools [#332](https://github.com/BU-ISCIII/buisciii-tools/pull/332). - Updated MAG lablogs and utils.py [#334](https://github.com/BU-ISCIII/buisciii-tools/pull/334). +- Updated some files (setup.py, __main__.py, README, etc) for the 2.2.0 release [#335](https://github.com/BU-ISCIII/buisciii-tools/pull/335). ### Modules From d846ab937e04093096836d515cac35105be8cadc Mon Sep 17 00:00:00 2001 From: victor5lm Date: Thu, 12 Sep 2024 10:35:05 +0200 Subject: [PATCH 8/8] Added 2.X.Xhot section to CHANGELOG.md --- CHANGELOG.md | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c2f9777fa..4ee3575ed 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,26 @@ Code contributions to the new version: ### Requirements +## [2.X.Xhot] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.1 + +### Credits + +Code contributions to the hotfix: + +### Template fixes and updates + +### Modules + +#### Added enhancements + +#### Fixes + +#### Changed + +#### Removed + +### Requirements + ## [2.2.0] - 2024-09-12 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.0 ### Credits