From 7b5815143266d95cf69e0142c0c47d244ccb26df Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Wed, 18 Sep 2024 16:55:38 -0600 Subject: [PATCH 01/17] Add files via upload --- recipes/hsdecipher/build.sh | 16 ++++++++++++++++ recipes/hsdecipher/meta.yaml | 29 +++++++++++++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 recipes/hsdecipher/build.sh create mode 100644 recipes/hsdecipher/meta.yaml diff --git a/recipes/hsdecipher/build.sh b/recipes/hsdecipher/build.sh new file mode 100644 index 0000000000000..795b50b513a02 --- /dev/null +++ b/recipes/hsdecipher/build.sh @@ -0,0 +1,16 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin + +cp HSD_heatmap.py $PREFIX/bin/hsd_heatmap + +cp HSD_add_on.py $PREFIX/bin/HSD_add_on.py +cp HSD_batch_run.py $PREFIX/bin/HSD_batch_run.py +cp HSD_categories.py $PREFIX/bin/HSD_categories.py +cp ko.tsv $PREFIX/bin/ko.tsv + +chmod a+x $PREFIX/bin/hsd_heatmap +chmod a+x $PREFIX/bin/HSD_add_on.py +chmod a+x $PREFIX/bin/HSD_batch_run.py +chmod a+x $PREFIX/bin/HSD_categories.py + diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml new file mode 100644 index 0000000000000..e7e1dc1d3e223 --- /dev/null +++ b/recipes/hsdecipher/meta.yaml @@ -0,0 +1,29 @@ +package: + name: hsdecipher + version: 1.0.0 +source: + url: https://github.com/zx0223winner/hsdecipher_conda/archive/refs/tags/hsdecipher.tar.gz + sha256: d852de0a394cecf09a3f76807b36ad549542322248426edada3876be350c25db +build: + noarch: python + number: '0' + run_exports: + - hsdecipher >=1.0.0 +requirements: + build: [] + run: + - python >=3.7 + - pandas + - seaborn + - matplotlib +test: + commands: + - $PREFIX/bin/hsd_heatmap -h +about: + home: https://github.com/zx0223winner/HSDecipher + summary: Pipeline for the downstream analysis of highly similar duplicate genes + license: GPL-3.0-or-later +extra: + copy_test_source_files: true + final: true + From f7462a4c2a64560fdbd6bf1e10dfa07ee7b45716 Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Wed, 18 Sep 2024 22:15:09 -0600 Subject: [PATCH 02/17] Update meta.yaml --- recipes/hsdecipher/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index e7e1dc1d3e223..a6b03000c968d 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -10,7 +10,6 @@ build: run_exports: - hsdecipher >=1.0.0 requirements: - build: [] run: - python >=3.7 - pandas From 6e8386c7dd23183d77d99cc70b8a383242026031 Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Thu, 19 Sep 2024 12:29:35 -0600 Subject: [PATCH 03/17] Delete recipes/hsdecipher/build.sh --- recipes/hsdecipher/build.sh | 16 ---------------- 1 file changed, 16 deletions(-) delete mode 100644 recipes/hsdecipher/build.sh diff --git a/recipes/hsdecipher/build.sh b/recipes/hsdecipher/build.sh deleted file mode 100644 index 795b50b513a02..0000000000000 --- a/recipes/hsdecipher/build.sh +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/bash - -mkdir -p $PREFIX/bin - -cp HSD_heatmap.py $PREFIX/bin/hsd_heatmap - -cp HSD_add_on.py $PREFIX/bin/HSD_add_on.py -cp HSD_batch_run.py $PREFIX/bin/HSD_batch_run.py -cp HSD_categories.py $PREFIX/bin/HSD_categories.py -cp ko.tsv $PREFIX/bin/ko.tsv - -chmod a+x $PREFIX/bin/hsd_heatmap -chmod a+x $PREFIX/bin/HSD_add_on.py -chmod a+x $PREFIX/bin/HSD_batch_run.py -chmod a+x $PREFIX/bin/HSD_categories.py - From f6181bda453b0a25bcdbcaf46875d62dc6c60a71 Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Thu, 19 Sep 2024 12:36:55 -0600 Subject: [PATCH 04/17] Update meta.yaml --- recipes/hsdecipher/meta.yaml | 34 +++++++++++++++++++--------------- 1 file changed, 19 insertions(+), 15 deletions(-) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index a6b03000c968d..4eee9fdc31b09 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -1,14 +1,21 @@ -package: - name: hsdecipher - version: 1.0.0 -source: - url: https://github.com/zx0223winner/hsdecipher_conda/archive/refs/tags/hsdecipher.tar.gz - sha256: d852de0a394cecf09a3f76807b36ad549542322248426edada3876be350c25db -build: - noarch: python - number: '0' - run_exports: - - hsdecipher >=1.0.0 +{% set name = "HSDecipher" %} + {% set version = "1.0.0" %} + + package: + name: {{ name|lower }} + version: {{ version }} + + source: + url: https://github.com/zx0223winner/{{name|lower}}_conda/archive/refs/tags/v{{version}}.tar.gz + sha256: f0b6abff9843acd1ef00e1753eeaf21179102d2e603bde01fb9cac2905fb975d + + build: + number: 0 + noarch: python + script: bash conda_build_package.sh + run_exports: + - {{ pin_subpackage('busco_phylogenomics', max_pin=None) }} + requirements: run: - python >=3.7 @@ -17,12 +24,9 @@ requirements: - matplotlib test: commands: - - $PREFIX/bin/hsd_heatmap -h + - hsd_heatmap -h about: home: https://github.com/zx0223winner/HSDecipher summary: Pipeline for the downstream analysis of highly similar duplicate genes license: GPL-3.0-or-later -extra: - copy_test_source_files: true - final: true From 822fe157e2ed9e9421ea1f638f274f8279916a9d Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Thu, 19 Sep 2024 12:46:09 -0600 Subject: [PATCH 05/17] Update meta.yaml --- recipes/hsdecipher/meta.yaml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index 4eee9fdc31b09..f01c5a1af302f 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -1,20 +1,20 @@ {% set name = "HSDecipher" %} - {% set version = "1.0.0" %} +{% set version = "1.0.0" %} - package: - name: {{ name|lower }} - version: {{ version }} +package: + name: {{ name|lower }} + version: {{ version }} - source: - url: https://github.com/zx0223winner/{{name|lower}}_conda/archive/refs/tags/v{{version}}.tar.gz - sha256: f0b6abff9843acd1ef00e1753eeaf21179102d2e603bde01fb9cac2905fb975d +source: + url: https://github.com/zx0223winner/{{name|lower}}_conda/archive/refs/tags/v{{version}}.tar.gz + sha256: f0b6abff9843acd1ef00e1753eeaf21179102d2e603bde01fb9cac2905fb975d - build: - number: 0 - noarch: python - script: bash conda_build_package.sh - run_exports: - - {{ pin_subpackage('busco_phylogenomics', max_pin=None) }} +build: + number: 0 + noarch: python + script: bash conda_build_package.sh + run_exports: + - {{ pin_subpackage('hsdecipher', max_pin=None) }} requirements: run: From cc6c15ee372ddab7ecb05767fa7d227b88295913 Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Thu, 19 Sep 2024 12:55:20 -0600 Subject: [PATCH 06/17] Update meta.yaml --- recipes/hsdecipher/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index f01c5a1af302f..faa5a1859459f 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -14,7 +14,7 @@ build: noarch: python script: bash conda_build_package.sh run_exports: - - {{ pin_subpackage('hsdecipher', max_pin=None) }} + - {{ pin_subpackage(name|lower, max_pin="x") }} requirements: run: From 2ec971a9af58d564f21713a3f06f0589262cf083 Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Thu, 19 Sep 2024 13:01:48 -0600 Subject: [PATCH 07/17] Update meta.yaml From a8d5fa713b31dfc697465db455a5c6f959825456 Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Thu, 19 Sep 2024 14:14:17 -0600 Subject: [PATCH 08/17] Update meta.yaml --- recipes/hsdecipher/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index faa5a1859459f..b9ba4a135a979 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -29,4 +29,5 @@ about: home: https://github.com/zx0223winner/HSDecipher summary: Pipeline for the downstream analysis of highly similar duplicate genes license: GPL-3.0-or-later + license_file: licence From 714f69a17dec438c9c42483184607cadae928989 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 24 Sep 2024 15:03:47 +0300 Subject: [PATCH 09/17] Use matplotlib-base --- recipes/hsdecipher/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index b9ba4a135a979..2ed7e59895adc 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -21,7 +21,7 @@ requirements: - python >=3.7 - pandas - seaborn - - matplotlib + - matplotlib-base test: commands: - hsd_heatmap -h From bd346df1e25c48161ef9515d5de0319f18676b88 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 24 Sep 2024 15:20:03 +0300 Subject: [PATCH 10/17] Update SHA --- recipes/hsdecipher/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index 2ed7e59895adc..1c09c04b459a4 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -7,7 +7,7 @@ package: source: url: https://github.com/zx0223winner/{{name|lower}}_conda/archive/refs/tags/v{{version}}.tar.gz - sha256: f0b6abff9843acd1ef00e1753eeaf21179102d2e603bde01fb9cac2905fb975d + sha256: ea5eec38927972070d65d126d410b6059ef0d1d8ef8fa5db23fa045c5e749543 build: number: 0 From 6ebe29f803c9739715327e3af7d32019fd7e6e84 Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Fri, 27 Sep 2024 11:46:52 -0600 Subject: [PATCH 11/17] Update meta.yaml --- recipes/hsdecipher/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index 1c09c04b459a4..3247097860dec 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -7,7 +7,7 @@ package: source: url: https://github.com/zx0223winner/{{name|lower}}_conda/archive/refs/tags/v{{version}}.tar.gz - sha256: ea5eec38927972070d65d126d410b6059ef0d1d8ef8fa5db23fa045c5e749543 + sha256: 8d044adab8b8476ef557a5c72adb9385680ed1cb6d3c407fd55293cf8bb23b95 build: number: 0 @@ -24,10 +24,10 @@ requirements: - matplotlib-base test: commands: - - hsd_heatmap -h + - hsdecipher -h about: home: https://github.com/zx0223winner/HSDecipher summary: Pipeline for the downstream analysis of highly similar duplicate genes + description: "Many tools have been developed to measure the degree of similarity between gene duplicates within and between species. Here, we present HSDecipher, a bioinformatics pipeline to assist users in the analysis and visualization of highly similar duplicate genes (HSDs). We describe the steps for analysis of HSDs statistics, expanding HSD gene set, and visualizing the results of comparative genomic analyses. HSDecipher represents a useful tool for researchers exploring the evolution of duplicate genes in select eukaryotic species." license: GPL-3.0-or-later license_file: licence - From bb3688c5b7f22b722eef5b1e279fffb5480d01ac Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Fri, 27 Sep 2024 13:17:17 -0600 Subject: [PATCH 12/17] Update meta.yaml --- recipes/hsdecipher/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index 3247097860dec..149fde7867c80 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -30,4 +30,4 @@ about: summary: Pipeline for the downstream analysis of highly similar duplicate genes description: "Many tools have been developed to measure the degree of similarity between gene duplicates within and between species. Here, we present HSDecipher, a bioinformatics pipeline to assist users in the analysis and visualization of highly similar duplicate genes (HSDs). We describe the steps for analysis of HSDs statistics, expanding HSD gene set, and visualizing the results of comparative genomic analyses. HSDecipher represents a useful tool for researchers exploring the evolution of duplicate genes in select eukaryotic species." license: GPL-3.0-or-later - license_file: licence + license_file: license From 53b4b73474217e00843c3b5429e99cb2c1986f0b Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Fri, 27 Sep 2024 13:18:43 -0600 Subject: [PATCH 13/17] Update meta.yaml --- recipes/hsdecipher/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index 149fde7867c80..d548558f25b22 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -28,6 +28,6 @@ test: about: home: https://github.com/zx0223winner/HSDecipher summary: Pipeline for the downstream analysis of highly similar duplicate genes - description: "Many tools have been developed to measure the degree of similarity between gene duplicates within and between species. Here, we present HSDecipher, a bioinformatics pipeline to assist users in the analysis and visualization of highly similar duplicate genes (HSDs). We describe the steps for analysis of HSDs statistics, expanding HSD gene set, and visualizing the results of comparative genomic analyses. HSDecipher represents a useful tool for researchers exploring the evolution of duplicate genes in select eukaryotic species." + description: "Many tools have been developed to measure the degree of similarity between gene duplicates within and between species.Here, we present HSDecipher, a bioinformatics pipeline to assist users in the analysis and visualization of highly similar duplicate genes (HSDs). We describe the steps for analysis of HSDs statistics, expanding HSD gene set, and visualizing the results of comparative genomic analyses. HSDecipher represents a useful tool for researchers exploring the evolution of duplicate genes in select eukaryotic species." license: GPL-3.0-or-later license_file: license From f17e4f38f6364ffa5b707527744c5ab82b69c390 Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Fri, 27 Sep 2024 13:28:56 -0600 Subject: [PATCH 14/17] Update meta.yaml --- recipes/hsdecipher/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index a6604153963ec..029e622c8fec3 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -7,7 +7,7 @@ package: source: url: https://github.com/zx0223winner/{{name|lower}}_conda/archive/refs/tags/v{{version}}.tar.gz - sha256: 8d044adab8b8476ef557a5c72adb9385680ed1cb6d3c407fd55293cf8bb23b95 + sha256: ea5eec38927972070d65d126d410b6059ef0d1d8ef8fa5db23fa045c5e749543 build: number: 0 From 5b0f8281a3fd47007b3b593b2f35caf58d85e089 Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Fri, 27 Sep 2024 13:40:56 -0600 Subject: [PATCH 15/17] Update meta.yaml --- recipes/hsdecipher/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index 029e622c8fec3..a6604153963ec 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -7,7 +7,7 @@ package: source: url: https://github.com/zx0223winner/{{name|lower}}_conda/archive/refs/tags/v{{version}}.tar.gz - sha256: ea5eec38927972070d65d126d410b6059ef0d1d8ef8fa5db23fa045c5e749543 + sha256: 8d044adab8b8476ef557a5c72adb9385680ed1cb6d3c407fd55293cf8bb23b95 build: number: 0 From e0155ba1e54435f92b29f2b4c81801ca97a803c0 Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Fri, 27 Sep 2024 14:16:50 -0600 Subject: [PATCH 16/17] Update meta.yaml --- recipes/hsdecipher/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index a6604153963ec..6f433598963d2 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8d044adab8b8476ef557a5c72adb9385680ed1cb6d3c407fd55293cf8bb23b95 build: - number: 0 + number: 1 noarch: python script: bash conda_build_package.sh run_exports: From 56a48945e8d9e7ec8d27630be3020bb7a7fddd35 Mon Sep 17 00:00:00 2001 From: Xi Zhang <13602037587@163.com> Date: Fri, 27 Sep 2024 14:43:46 -0600 Subject: [PATCH 17/17] Update meta.yaml --- recipes/hsdecipher/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml index 6f433598963d2..e03d9d9cfca9c 100644 --- a/recipes/hsdecipher/meta.yaml +++ b/recipes/hsdecipher/meta.yaml @@ -7,7 +7,7 @@ package: source: url: https://github.com/zx0223winner/{{name|lower}}_conda/archive/refs/tags/v{{version}}.tar.gz - sha256: 8d044adab8b8476ef557a5c72adb9385680ed1cb6d3c407fd55293cf8bb23b95 + sha256: 54ab84f8584c69a50db4678b49279b0a0b4b05cf0028eec9c2f2ea2205917b76 build: number: 1