version 1.0.2 release

Kelly-ST-HRI · Nov 2, 2022 · feb3186 · feb3186
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -21,15 +21,15 @@ 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:
 
 @Manual{,
     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
@@ -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
@@ -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;