From feb3186017a2799d1068d8504e7a121d4722df36 Mon Sep 17 00:00:00 2001 From: Simon Thomas Kelly Date: Wed, 2 Nov 2022 16:50:35 +0900 Subject: [PATCH] version 1.0.2 release --- README.md | 6 +++--- README.txt | 6 +++--- RELEASE_NOTES.txt | 9 ++++++++- citation.cff | 2 +- citation.md | 4 ++-- citation.txt | 4 ++-- docs/index.rst | 2 +- hicup_module.pm | 2 +- 8 files changed, 21 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index a88b508..8d92a6e 100644 --- a/README.md +++ b/README.md @@ -36,7 +36,7 @@ Contact: Contact the software author to discuss the software, report bugs or suggest enhancements at: https://github.com/StevenWingett/HiCUP/issues -HiCUP+ (v1.0.1) maintainer: S. Thomas Kelly +HiCUP+ (v1.0.2) maintainer: S. Thomas Kelly Contact: simonthomas.kelly [at] hugp [dot] com @@ -88,7 +88,7 @@ BibTeX version: The software release can be cited as follows: > Kelly, S. T. & Yuhara, S. (2022) HiCUP+: a fast open-source pipeline for accurately processing large scale Hi-C sequence data. -> Software release v1.0.1 URL: [https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/) +> Software release v1.0.2 URL: [https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/) BibTex version: @@ -97,7 +97,7 @@ BibTex version: author = {Kelly, S. Thomas and Yuhara, Satoshi}, title = {{H}i{C}{U}{P}-{P}lus: a fast open-source pipeline for accurately processing large scale {H}i-{C} sequence data}}, year = {2022}, - note = {Software release version v1.0.1}, + note = {Software release version v1.0.2}, url = {[https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/)}, } ``` diff --git a/README.txt b/README.txt index 040368b..16cae69 100644 --- a/README.txt +++ b/README.txt @@ -36,7 +36,7 @@ Contact: Contact the software author to discuss the software, report bugs or suggest enhancements at: https://github.com/StevenWingett/HiCUP/issues -HiCUP+ (v1.0.1) maintainer: S. Thomas Kelly +HiCUP+ (v1.0.2) maintainer: S. Thomas Kelly Contact: simonthomas.kelly [at] hugp [dot] com @@ -88,7 +88,7 @@ BibTeX version: The software release can be cited as follows: > Kelly, S. T. & Yuhara, S. (2022) HiCUP+: a fast open-source pipeline for accurately processing large scale Hi-C sequence data. -> Software release v1.0.1 URL: [https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/) +> Software release v1.0.2 URL: [https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/) BibTex version: @@ -97,7 +97,7 @@ BibTex version: author = {Kelly, S. Thomas and Yuhara, Satoshi}, title = {{H}i{C}{U}{P}-{P}lus: a fast open-source pipeline for accurately processing large scale {H}i-{C} sequence data}}, year = {2022}, - note = {Software release version v1.0.1}, + note = {Software release version v1.0.2}, url = {[https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/)}, } ``` diff --git a/RELEASE_NOTES.txt b/RELEASE_NOTES.txt index f7a0a4b..33befe0 100644 --- a/RELEASE_NOTES.txt +++ b/RELEASE_NOTES.txt @@ -1,4 +1,11 @@ -RELEASE NOTES FOR HICUP-Plus v1.0.1 (11 MARCH 2022) + +RELEASE NOTES FOR HICUP-Plus v1.0.2 (2 NOVEMBER 2022) + +HiCUP+ v1.0.2 is a mnior update incorporating the changes described below: + +- updated checks in the HiCUP modules to check for SSH connections + +- updated Dragen call to run via SSH if hostname does not include "dragen" ------------------------------------------------- diff --git a/citation.cff b/citation.cff index bf95ab4..fbdab22 100644 --- a/citation.cff +++ b/citation.cff @@ -13,7 +13,7 @@ authors: affiliation: "H.U. Group Research Institute, G.K., Fuchigami 50, Akiruno, Tokyo, Japan" affiliation: "SRL, Inc., Fuchigami 50, Akiruno, Tokyo, Japan" orcid: "http://orcid.org/0000-0003-1375-3848" -version: 1.0.1 +version: 1.0.2 doi: 10.1101/2022.05.18.492393 date-released: 2022-03-11 url: "https://github.com/hugp-ri/hicup-plus" diff --git a/citation.md b/citation.md index fa886ab..80c6e5b 100644 --- a/citation.md +++ b/citation.md @@ -25,7 +25,7 @@ BibTeX version: The software release can be cited as follows: > Kelly, S. T. & Yuhara, S. (2022) HiCUP+: a fast open-source pipeline for accurately processing large scale Hi-C sequence data. -> Software release v1.0.1 URL: [https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/) +> Software release v1.0.2 URL: [https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/) BibTex version: @@ -34,7 +34,7 @@ BibTex version: author = {Kelly, S. Thomas and Yuhara, Satoshi}, title = {{H}i{C}{U}{P}-{P}lus: a fast open-source pipeline for accurately processing large scale {H}i-{C} sequence data}}, year = {2022}, - note = {Software release version v1.0.1}, + note = {Software release version v1.0.2}, url = {[https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/)}, } ``` diff --git a/citation.txt b/citation.txt index 106c668..ab06d67 100644 --- a/citation.txt +++ b/citation.txt @@ -21,7 +21,7 @@ BibTeX version: The software release can be cited as follows: Kelly, S. T. & Yuhara, S. (2022) HiCUP+: a fast open-source pipeline for accurately processing large scale Hi-C sequence data. -Software release v1.0.1 URL: https://github.com/hugp-ri/hicup-plus/ +Software release v1.0.2 URL: https://github.com/hugp-ri/hicup-plus/ BibTex version: @@ -29,7 +29,7 @@ BibTex version: author = {Kelly, S. Thomas and Yuhara, Satoshi}, title = {{H}i{C}{U}{P}-{P}lus: a fast open-source pipeline for accurately processing large scale {H}i-{C} sequence data}}, year = {2022}, - note = {Software release version v1.0.1}, + note = {Software release version v1.0.2}, url = {https://github.com/hugp-ri/hicup-plus/}, } diff --git a/docs/index.rst b/docs/index.rst index 88142c0..4da1138 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -984,7 +984,7 @@ BibTex version: author = {Kelly, S. Thomas and Yuhara, Satoshi}, title = {{H}i{C}{U}{P}-{P}lus: a fast open-source pipeline for accurately processing large scale {H}i-{C} sequence data}}, year = {2022}, - note = {Software release version v1.0.1}, + note = {Software release version v1.0.2}, url = {https://github.com/hugp-ri/hicup-plus/}, } diff --git a/hicup_module.pm b/hicup_module.pm index 66f3165..6ab1465 100644 --- a/hicup_module.pm +++ b/hicup_module.pm @@ -8,7 +8,7 @@ our @EXPORT = qw(VERSION hasval deduplicate_array checkR process_config check_fi our @EXPORT_OK = qw(hashVal outdirFileNamer check_no_duplicate_filename check_filenames_ok checkAligner checkAlignerIndices newopen quality_checker determineAlignerFormat get_csome_position); -our $VERSION = "1.0.1"; +our $VERSION = "1.0.2"; use Data::Dumper; use strict;