From 0d222793500ef5d5bb01bdb6029fba6cb537cb72 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 2 Jul 2024 21:11:46 +0000 Subject: [PATCH 01/20] Update primerforge to 1.2.5 --- recipes/primerforge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index ee7e23d85787f..20a5a81158d34 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "1.1.1" %} +{% set version = "1.2.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: b13a26e006f7790f80937178a311cfbb95a9f69ee8ab97a0d21139bd197fec13 + sha256: 428a2712466a7c64296c893cb525ab092dd943ace5728b8c09e3c0c7bfe15300 build: number: 0 From b5d778c4e894b326fa34120e189659bcf32ea91b Mon Sep 17 00:00:00 2001 From: "Joe Wirth (Joseph S. Wirth)" <71667025+dr-joe-wirth@users.noreply.github.com> Date: Tue, 2 Jul 2024 17:36:23 -0400 Subject: [PATCH 02/20] added `khmer` as a dependency --- recipes/primerforge/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index 20a5a81158d34..c5f5724a6d9a4 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -28,6 +28,8 @@ requirements: - numpy - primer3-py >=2.0 - scipy >=1.10 + - pip: + - khmer >=2.1 test: commands: From f1f32a35b392cee7a8ab07c747f5a40eb19958bb Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 3 Jul 2024 10:11:29 +0300 Subject: [PATCH 03/20] Fix yaml syntax --- recipes/primerforge/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index c5f5724a6d9a4..aa447de84cf36 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -28,8 +28,7 @@ requirements: - numpy - primer3-py >=2.0 - scipy >=1.10 - - pip: - - khmer >=2.1 + - khmer >=2.1 test: commands: From 4226fd16e6b0e7154267187c10375100696624f9 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 3 Jul 2024 10:29:45 +0300 Subject: [PATCH 04/20] Ping kmer between 2.1 and 3 --- recipes/primerforge/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index aa447de84cf36..3bf9014defa59 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -28,7 +28,7 @@ requirements: - numpy - primer3-py >=2.0 - scipy >=1.10 - - khmer >=2.1 + - khmer >=2.1,<3 test: commands: From 3b58a113c066cc6e091a11eee27fd92667c2050e Mon Sep 17 00:00:00 2001 From: "Joe Wirth (Joseph S. Wirth)" <71667025+dr-joe-wirth@users.noreply.github.com> Date: Wed, 3 Jul 2024 13:49:39 -0400 Subject: [PATCH 05/20] updated compatible python versions --- recipes/primerforge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index 3bf9014defa59..2b9f8bc9170c0 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -20,10 +20,10 @@ build: requirements: host: - - python >=3.11 + - python >=3.9,<3.12 - pip run: - - python >=3.11 + - python >=3.9,<3.12 - biopython ==1.81 - numpy - primer3-py >=2.0 From f67865935112b48996c91ef7741d891bcd9815aa Mon Sep 17 00:00:00 2001 From: dr-joe-wirth Date: Wed, 3 Jul 2024 18:06:44 -0400 Subject: [PATCH 06/20] started working on a `build.sh` file...not yet working --- recipes/primerforge/build.sh | 11 +++++++++++ recipes/primerforge/meta.yaml | 3 +-- 2 files changed, 12 insertions(+), 2 deletions(-) create mode 100644 recipes/primerforge/build.sh diff --git a/recipes/primerforge/build.sh b/recipes/primerforge/build.sh new file mode 100644 index 0000000000000..9917414dea90b --- /dev/null +++ b/recipes/primerforge/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -e + +# Install primerforge using pip +python3 -m pip install $SRC_DIR --no-deps --no-build-isolation -vvv + +# Install khmer +wget https://github.com/dib-lab/khmer/archive/refs/tags/v2.1.1.tar.gz +tar xzf v2.1.1.tar.gz +cd khmer-2.1.1 +python3 setup.py install diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index 2b9f8bc9170c0..aea3d164656b6 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -12,7 +12,7 @@ source: build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + #script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv && {{ PYTHON }} -m pip install khmer" entry_points: - primerForge=bin.main:main run_exports: @@ -28,7 +28,6 @@ requirements: - numpy - primer3-py >=2.0 - scipy >=1.10 - - khmer >=2.1,<3 test: commands: From 0497ae5ddc62e37397afe66fc064bde00586e9fd Mon Sep 17 00:00:00 2001 From: dr-joe-wirth Date: Mon, 8 Jul 2024 11:00:22 -0400 Subject: [PATCH 07/20] removing attempts to install khmer with pip; recipe does not work --- recipes/primerforge/build.sh | 11 ----------- recipes/primerforge/meta.yaml | 3 ++- 2 files changed, 2 insertions(+), 12 deletions(-) delete mode 100644 recipes/primerforge/build.sh diff --git a/recipes/primerforge/build.sh b/recipes/primerforge/build.sh deleted file mode 100644 index 9917414dea90b..0000000000000 --- a/recipes/primerforge/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash -set -e - -# Install primerforge using pip -python3 -m pip install $SRC_DIR --no-deps --no-build-isolation -vvv - -# Install khmer -wget https://github.com/dib-lab/khmer/archive/refs/tags/v2.1.1.tar.gz -tar xzf v2.1.1.tar.gz -cd khmer-2.1.1 -python3 setup.py install diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index aea3d164656b6..6712a5aa986e1 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -12,7 +12,7 @@ source: build: number: 0 noarch: python - #script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv && {{ PYTHON }} -m pip install khmer" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" entry_points: - primerForge=bin.main:main run_exports: @@ -25,6 +25,7 @@ requirements: run: - python >=3.9,<3.12 - biopython ==1.81 + - khmer >=2.1.1 - numpy - primer3-py >=2.0 - scipy >=1.10 From fdb959469b736eeb544934477a167d4e4ddfd5a8 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jul 2024 21:06:32 +0000 Subject: [PATCH 08/20] Update primerforge to 1.2.7 --- recipes/primerforge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index 6712a5aa986e1..0442baf54ae41 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "1.2.5" %} +{% set version = "1.2.7" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 428a2712466a7c64296c893cb525ab092dd943ace5728b8c09e3c0c7bfe15300 + sha256: 27295871c8a3e0d51ec0dfc0776227d1e254e12ab94b4e9181d59295d2b0f81f build: number: 0 From e917499c339bbb69ab65fb41f9c7ae56cfa6d677 Mon Sep 17 00:00:00 2001 From: "Joe Wirth (Joseph S. Wirth)" <71667025+dr-joe-wirth@users.noreply.github.com> Date: Tue, 16 Jul 2024 21:33:48 -0400 Subject: [PATCH 09/20] Added `pyahocorasick` requirement --- recipes/primerforge/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index 0442baf54ae41..1ad12b4b3d0b0 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -28,6 +28,7 @@ requirements: - khmer >=2.1.1 - numpy - primer3-py >=2.0 + - pyahocorasick - scipy >=1.10 test: From 318594c17ba2f3cff5f41787df48699b0f52e539 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jul 2024 18:17:25 +0000 Subject: [PATCH 10/20] Update primerforge to 1.3.1 --- recipes/primerforge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index 1ad12b4b3d0b0..feeca7caee1f8 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "1.2.7" %} +{% set version = "1.3.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 27295871c8a3e0d51ec0dfc0776227d1e254e12ab94b4e9181d59295d2b0f81f + sha256: 497244b225c9f3c6604a824b61a25a25a885f5bf913e364c0eb2b38e7c1cf627 build: number: 0 From 236bd98736375511f82655822bf4e92e48d3a3eb Mon Sep 17 00:00:00 2001 From: "Joe Wirth (Joseph S. Wirth)" <71667025+dr-joe-wirth@users.noreply.github.com> Date: Mon, 29 Jul 2024 14:31:20 -0400 Subject: [PATCH 11/20] added `isPcr` dependency --- recipes/primerforge/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index feeca7caee1f8..ce000732e26d6 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -25,6 +25,7 @@ requirements: run: - python >=3.9,<3.12 - biopython ==1.81 + - ispcr - khmer >=2.1.1 - numpy - primer3-py >=2.0 From 59575cbc4b89d8a4f0a9b0034eb953b20ff932ac Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jul 2024 19:10:36 +0000 Subject: [PATCH 12/20] Update primerforge to 1.3.2 --- recipes/primerforge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index ce000732e26d6..97ca1efc1b288 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "1.3.1" %} +{% set version = "1.3.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 497244b225c9f3c6604a824b61a25a25a885f5bf913e364c0eb2b38e7c1cf627 + sha256: 6aa32a2b59b90390429a04689c7712420b38fc17443b809b95f167d2533dcefa build: number: 0 From 2fdc207ce5eb6a213cff4b177b701d49408663c4 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Aug 2024 18:15:36 +0000 Subject: [PATCH 13/20] Update primerforge to 1.3.3 --- recipes/primerforge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index 97ca1efc1b288..d13852591380b 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "1.3.2" %} +{% set version = "1.3.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 6aa32a2b59b90390429a04689c7712420b38fc17443b809b95f167d2533dcefa + sha256: a54faa2bdf583a988c0c08a88bbb93d870c9bb245f217f0bea11b0015199a9bc build: number: 0 From b1c925d55849a53c0104588e0726bc0ce24c3d1a Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Aug 2024 18:07:17 +0000 Subject: [PATCH 14/20] Update primerforge to 1.3.4 --- recipes/primerforge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index d13852591380b..b9fd5b2d4e61a 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "1.3.3" %} +{% set version = "1.3.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: a54faa2bdf583a988c0c08a88bbb93d870c9bb245f217f0bea11b0015199a9bc + sha256: fc11721a5ece13621c4eadec55d412ba18f89abd40bfb1a4c64a42fb45512089 build: number: 0 From fd8f362bf2c4ca11aa8224b848338d5a71e89255 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Aug 2024 22:16:06 +0000 Subject: [PATCH 15/20] Update primerforge to 1.3.5 --- recipes/primerforge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index b9fd5b2d4e61a..b44086ea8c8c5 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "1.3.4" %} +{% set version = "1.3.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: fc11721a5ece13621c4eadec55d412ba18f89abd40bfb1a4c64a42fb45512089 + sha256: 8d8c49186568541a6426da6042e1576c9250baeaabfbd078163325cb01feb483 build: number: 0 From 11a46198663c70aca26cb634d513a1c71ad4718d Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 22 Aug 2024 19:05:24 +0000 Subject: [PATCH 16/20] Update primerforge to 1.3.6 --- recipes/primerforge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index b44086ea8c8c5..0bcdf112d447a 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "1.3.5" %} +{% set version = "1.3.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 8d8c49186568541a6426da6042e1576c9250baeaabfbd078163325cb01feb483 + sha256: a37a225a278bd0a96c035b1c0a7d74a8c73d95aecf60e9dfbe246addd1f74b82 build: number: 0 From 4f3a8c97065d8a8a8f9ac95b1431dd92d18dcb74 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 16 Sep 2024 18:16:47 +0000 Subject: [PATCH 17/20] Update primerforge to 1.3.7 --- recipes/primerforge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index 0bcdf112d447a..0dbd546a77284 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "1.3.6" %} +{% set version = "1.3.7" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: a37a225a278bd0a96c035b1c0a7d74a8c73d95aecf60e9dfbe246addd1f74b82 + sha256: 9c80041491433ed5896104c402c9c2f739c4c4342aae090df40794fd42be1e8e build: number: 0 From 459b4a42e3c099ce16fa822535aa1dfb5ff4e50d Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 7 Oct 2024 19:14:10 +0000 Subject: [PATCH 18/20] Update primerforge to 1.4.3 --- recipes/primerforge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index 0dbd546a77284..a1a4178447f9d 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "1.3.7" %} +{% set version = "1.4.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9c80041491433ed5896104c402c9c2f739c4c4342aae090df40794fd42be1e8e + sha256: 80e858976d94c8fb8578a43c51da3700d2ba3718cdbb109cfe176f942e222ae6 build: number: 0 From 02a31d198ef77e20f62281191c696f383d7fd5da Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 9 Oct 2024 20:13:21 +0000 Subject: [PATCH 19/20] Update primerforge to 1.5.1 --- recipes/primerforge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index a1a4178447f9d..f9b7b2dbe4706 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "1.4.3" %} +{% set version = "1.5.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 80e858976d94c8fb8578a43c51da3700d2ba3718cdbb109cfe176f942e222ae6 + sha256: ec71ade593e9f3d342ac884ad469f4468540dbe61b9f9b0a932769195fcdf486 build: number: 0 From 221d997b350872cc376089dca4de1386b705a499 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Nov 2024 17:10:52 +0000 Subject: [PATCH 20/20] Update primerforge to 1.5.2 --- recipes/primerforge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index f9b7b2dbe4706..548538a95cbd0 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "1.5.1" %} +{% set version = "1.5.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: ec71ade593e9f3d342ac884ad469f4468540dbe61b9f9b0a932769195fcdf486 + sha256: 72e9caab79a87cab3319afb185ecc2a01c94d014a00eca6b62592eb67ab72ab3 build: number: 0