From 9f0367d67556f6faa0efcbb63d3899aac7dabc41 Mon Sep 17 00:00:00 2001
From: berkeucar <bucar.cs@gmail.com>
Date: Fri, 13 Sep 2024 23:00:05 -0700
Subject: [PATCH 01/13] Added DSSP package

---
 recipes/dssp/build.sh             | 23 ++++++++
 recipes/dssp/dssp-boost-tr1.patch | 87 +++++++++++++++++++++++++++++++
 recipes/dssp/meta.yaml            | 50 ++++++++++++++++++
 3 files changed, 160 insertions(+)
 create mode 100644 recipes/dssp/build.sh
 create mode 100644 recipes/dssp/dssp-boost-tr1.patch
 create mode 100644 recipes/dssp/meta.yaml

diff --git a/recipes/dssp/build.sh b/recipes/dssp/build.sh
new file mode 100644
index 0000000000000..2316905bb2de1
--- /dev/null
+++ b/recipes/dssp/build.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+set -e
+
+# Link dynamically
+sed -i -e 's/\-static //' makefile
+
+echo "DEST_DIR=${PREFIX}" > make.config
+echo "MAN_DIR=${PREFIX}/share/man/man1" >> make.config
+
+echo "BOOST_INC_DIR=${BUILD_PREFIX}/include" >> make.config
+echo "BOOST_LIB_DIR=${BUILD_PREFIX}/lib" >> make.config
+# Use conda-provided cxx
+sed -i -e 's/^CXX/#CXX/' makefile
+
+# clang++ won't find std::tuple unless in C++11 mode;
+# don't compile with anything newer than C++11 since we use the removed
+# std::unary_function
+if [ `uname -s` = "Darwin" ]; then
+  CFLAGS="-std=c++11 -Wno-enum-constexpr-conversion ${CFLAGS}"
+fi
+
+make -j4 install
diff --git a/recipes/dssp/dssp-boost-tr1.patch b/recipes/dssp/dssp-boost-tr1.patch
new file mode 100644
index 0000000000000..c924366dd79bc
--- /dev/null
+++ b/recipes/dssp/dssp-boost-tr1.patch
@@ -0,0 +1,87 @@
+diff -Nur dssp-3.0.0/src/dssp.cpp dssp-3.0.0-patched/src/dssp.cpp
+--- dssp-3.0.0/src/dssp.cpp	2017-09-21 02:42:09.000000000 -0700
++++ dssp-3.0.0-patched/src/dssp.cpp	2018-04-25 11:05:47.499486529 -0700
+@@ -73,7 +73,7 @@
+ 
+   double alpha;
+   char chirality;
+-  std::tr1::tie(alpha,chirality) = residue.Alpha();
++  std::tie(alpha,chirality) = residue.Alpha();
+ 
+   uint32 bp[2] = {};
+   char bridgelabel[2] = { ' ', ' ' };
+diff -Nur dssp-3.0.0/src/primitives-3d.cpp dssp-3.0.0-patched/src/primitives-3d.cpp
+--- dssp-3.0.0/src/primitives-3d.cpp	2017-09-21 02:42:09.000000000 -0700
++++ dssp-3.0.0-patched/src/primitives-3d.cpp	2018-04-25 11:05:54.642577464 -0700
+@@ -152,7 +152,7 @@
+ 
+ // --------------------------------------------------------------------
+ 
+-std::tr1::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q)
++std::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q)
+ {
+   if (q.R_component_1() > 1)
+     q = Normalize(q);
+@@ -168,7 +168,7 @@
+ 
+   MPoint axis(q.R_component_2() / s, q.R_component_3() / s, q.R_component_4() / s);
+ 
+-  return std::tr1::make_tuple(angle, axis);
++  return std::make_tuple(angle, axis);
+ }
+ 
+ MPoint CenterPoints(std::vector<MPoint>& points)
+diff -Nur dssp-3.0.0/src/primitives-3d.h dssp-3.0.0-patched/src/primitives-3d.h
+--- dssp-3.0.0/src/primitives-3d.h	2017-09-21 02:42:09.000000000 -0700
++++ dssp-3.0.0-patched/src/primitives-3d.h	2018-04-25 11:05:18.542117901 -0700
+@@ -12,7 +12,7 @@
+ #pragma once
+ 
+ #include <boost/math/quaternion.hpp>
+-#include <boost/tr1/tuple.hpp>
++#include <tuple>
+ 
+ #include <vector>
+ 
+@@ -71,7 +71,7 @@
+ 
+ MQuaternion Normalize(MQuaternion q);
+ 
+-std::tr1::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q);
++std::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q);
+ MPoint Centroid(std::vector<MPoint>& points);
+ MPoint CenterPoints(std::vector<MPoint>& points);
+ MQuaternion AlignPoints(const std::vector<MPoint>& a,
+diff -Nur dssp-3.0.0/src/structure.cpp dssp-3.0.0-patched/src/structure.cpp
+--- dssp-3.0.0/src/structure.cpp	2017-09-21 02:42:09.000000000 -0700
++++ dssp-3.0.0-patched/src/structure.cpp	2018-04-25 11:05:41.581411192 -0700
+@@ -554,7 +554,7 @@
+   return result;
+ }
+ 
+-std::tr1::tuple<double,char> MResidue::Alpha() const
++std::tuple<double,char> MResidue::Alpha() const
+ {
+   double alhpa = 360;
+   char chirality = ' ';
+@@ -571,7 +571,7 @@
+     else
+       chirality = '+';
+   }
+-  return std::tr1::make_tuple(alhpa, chirality);
++  return std::make_tuple(alhpa, chirality);
+ }
+ 
+ double MResidue::Kappa() const
+diff -Nur dssp-3.0.0/src/structure.h dssp-3.0.0-patched/src/structure.h
+--- dssp-3.0.0/src/structure.h	2017-09-21 02:42:09.000000000 -0700
++++ dssp-3.0.0-patched/src/structure.h	2018-04-25 11:05:03.233921919 -0700
+@@ -171,7 +171,7 @@
+ 
+   double        Phi() const;
+   double        Psi() const;
+-  std::tr1::tuple<double,char>
++  std::tuple<double,char>
+             Alpha() const;
+   double        Kappa() const;
+   double        TCO() const;
diff --git a/recipes/dssp/meta.yaml b/recipes/dssp/meta.yaml
new file mode 100644
index 0000000000000..9c21821218f60
--- /dev/null
+++ b/recipes/dssp/meta.yaml
@@ -0,0 +1,50 @@
+# This file, the patch file and build file were taken from conda salilab channel's recipes - please see https://github.com/salilab/conda-recipes for more.
+package:
+  name: dssp
+  version: "3.0.0"
+
+source:
+  fn: dssp-3.0.0.tgz
+# url: ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-3.0.0.tgz
+# Original site appears to be down - use our mirror:
+  url: https://salilab.org/dssp/dssp-3.0.0.tgz
+  sha256: 25d39a2107767b622a59dd9fa790112c1516564b8518fc6ac0fab081d5ac3ab0
+  patches:
+    - dssp-boost-tr1.patch #Rebuild with latest gcc and boost - this was taken from the 
+
+build:
+  number: 1
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - boost-cpp
+    - zlib
+    - bzip2
+  run:
+    - {{ pin_compatible('boost-cpp') }}
+
+about:
+  home: http://swift.cmbi.ru.nl/gv/dssp/
+  summary: 'Secondary structure assignment'
+  license: Boost
+  description: >
+    The DSSP program was designed by Wolfgang Kabsch and Chris Sander to
+    standardize secondary structure assignment. DSSP is a database of secondary
+    structure assignments (and much more) for all protein entries in the Protein
+    Data Bank (PDB). DSSP is also the program that calculates DSSP entries from
+    PDB entries. DSSP does not predict secondary structure.
+
+    Note that this is a very old version of DSSP, which we have used in the
+    past. It is kept here in the hope that others may find it useful - but
+    it may not work on newer systems (e.g. Apple Silicon Macs). We recommend
+    using the most recent version of DSSP instead.
+    See [the DSSP website](http://swift.cmbi.ru.nl/gv/dssp/) for more details.
+
+    If you have problems with this conda package, please
+    [open an issue](https://github.com/salilab/conda-recipes/issues).
+
+test:
+  commands:
+    - mkdssp --version

From 159ae822499cbce719062780dec14728688ef199 Mon Sep 17 00:00:00 2001
From: berkeucar <bucar.cs@gmail.com>
Date: Fri, 13 Sep 2024 23:26:55 -0700
Subject: [PATCH 02/13] added run_exports section

---
 recipes/dssp/meta.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/recipes/dssp/meta.yaml b/recipes/dssp/meta.yaml
index 9c21821218f60..91d6884f1def1 100644
--- a/recipes/dssp/meta.yaml
+++ b/recipes/dssp/meta.yaml
@@ -24,6 +24,8 @@ requirements:
     - bzip2
   run:
     - {{ pin_compatible('boost-cpp') }}
+  run_exports:
+    - {{ pin_subpackage('DSSP', max_pin="x.x") }}
 
 about:
   home: http://swift.cmbi.ru.nl/gv/dssp/

From 3c942a0922e114b5497983721711fe7a4978de22 Mon Sep 17 00:00:00 2001
From: berkeucar <bucar.cs@gmail.com>
Date: Fri, 13 Sep 2024 23:34:09 -0700
Subject: [PATCH 03/13] fixed run_exports section

---
 recipes/dssp/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/dssp/meta.yaml b/recipes/dssp/meta.yaml
index 91d6884f1def1..1f5140a294585 100644
--- a/recipes/dssp/meta.yaml
+++ b/recipes/dssp/meta.yaml
@@ -14,6 +14,8 @@ source:
 
 build:
   number: 1
+  run_exports:
+    - {{ pin_subpackage('DSSP', max_pin="x.x") }}
 
 requirements:
   build:
@@ -24,8 +26,6 @@ requirements:
     - bzip2
   run:
     - {{ pin_compatible('boost-cpp') }}
-  run_exports:
-    - {{ pin_subpackage('DSSP', max_pin="x.x") }}
 
 about:
   home: http://swift.cmbi.ru.nl/gv/dssp/

From 866be995d23738520a6dd84fcfb655dd4dd3290d Mon Sep 17 00:00:00 2001
From: berkeucar <bucar.cs@gmail.com>
Date: Fri, 13 Sep 2024 23:41:13 -0700
Subject: [PATCH 04/13] fixed the build number

---
 recipes/dssp/meta.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/recipes/dssp/meta.yaml b/recipes/dssp/meta.yaml
index 1f5140a294585..db038121454da 100644
--- a/recipes/dssp/meta.yaml
+++ b/recipes/dssp/meta.yaml
@@ -1,10 +1,11 @@
+{% set version = "3.0.0" %}
 # This file, the patch file and build file were taken from conda salilab channel's recipes - please see https://github.com/salilab/conda-recipes for more.
 package:
   name: dssp
-  version: "3.0.0"
+  version: {{ version }}
 
 source:
-  fn: dssp-3.0.0.tgz
+  fn: dssp-{{ version }}.tgz
 # url: ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-3.0.0.tgz
 # Original site appears to be down - use our mirror:
   url: https://salilab.org/dssp/dssp-3.0.0.tgz
@@ -13,7 +14,7 @@ source:
     - dssp-boost-tr1.patch #Rebuild with latest gcc and boost - this was taken from the 
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('DSSP', max_pin="x.x") }}
 

From 30e0d066c4af06b35221128f4194698d424d1be4 Mon Sep 17 00:00:00 2001
From: berkeucar <bucar.cs@gmail.com>
Date: Fri, 13 Sep 2024 23:49:53 -0700
Subject: [PATCH 05/13] removed fn section

---
 recipes/dssp/meta.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/recipes/dssp/meta.yaml b/recipes/dssp/meta.yaml
index db038121454da..1717a56c2000c 100644
--- a/recipes/dssp/meta.yaml
+++ b/recipes/dssp/meta.yaml
@@ -5,9 +5,6 @@ package:
   version: {{ version }}
 
 source:
-  fn: dssp-{{ version }}.tgz
-# url: ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-3.0.0.tgz
-# Original site appears to be down - use our mirror:
   url: https://salilab.org/dssp/dssp-3.0.0.tgz
   sha256: 25d39a2107767b622a59dd9fa790112c1516564b8518fc6ac0fab081d5ac3ab0
   patches:

From d93fd923d2f12ac5c4d2192b66b1bd607ff3a8c5 Mon Sep 17 00:00:00 2001
From: berkeucar <bucar.cs@gmail.com>
Date: Sat, 14 Sep 2024 00:05:16 -0700
Subject: [PATCH 06/13] fixed pin_subpackages section

---
 recipes/dssp/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/dssp/meta.yaml b/recipes/dssp/meta.yaml
index 1717a56c2000c..5ac472fe91748 100644
--- a/recipes/dssp/meta.yaml
+++ b/recipes/dssp/meta.yaml
@@ -13,7 +13,7 @@ source:
 build:
   number: 0
   run_exports:
-    - {{ pin_subpackage('DSSP', max_pin="x.x") }}
+    - {{ pin_subpackage('dssp', max_pin="x.x") }}
 
 requirements:
   build:

From 8125ca07d60b58452b88eb34f09ff65d81820758 Mon Sep 17 00:00:00 2001
From: berkeucar <bucar.cs@gmail.com>
Date: Sat, 14 Sep 2024 10:57:48 -0700
Subject: [PATCH 07/13] added make to the meta.yml

---
 recipes/dssp/meta.yaml   |  1 +
 recipes/tamper/build.sh  | 33 ++++++++++++++++++++++++++++
 recipes/tamper/meta.yaml | 47 ++++++++++++++++++++++++++++++++++++++++
 3 files changed, 81 insertions(+)
 create mode 100644 recipes/tamper/build.sh
 create mode 100644 recipes/tamper/meta.yaml

diff --git a/recipes/dssp/meta.yaml b/recipes/dssp/meta.yaml
index 5ac472fe91748..ec9d72728cf70 100644
--- a/recipes/dssp/meta.yaml
+++ b/recipes/dssp/meta.yaml
@@ -22,6 +22,7 @@ requirements:
     - boost-cpp
     - zlib
     - bzip2
+    - make
   run:
     - {{ pin_compatible('boost-cpp') }}
 
diff --git a/recipes/tamper/build.sh b/recipes/tamper/build.sh
new file mode 100644
index 0000000000000..0c87f849ba1e0
--- /dev/null
+++ b/recipes/tamper/build.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+mkdir -p ${PREFIX}/bin/
+mkdir -p ${PREFIX}/share/tamper/
+mkdir -p ${PREFIX}/share/tamper/src/
+mkdir -p ${PREFIX}/share/tamper/checkpoints/trained
+cp -r src/. ${PREFIX}/share/tamper/src/
+cp -r checkpoints/trained/. ${PREFIX}/share/tamper/checkpoints/trained
+ls ${PREFIX}/share/tamper/src/
+
+#This allows src code to be executbale for user and group
+chmod -R u+x ${PREFIX}/share/tamper/src/
+chmod -R g+x ${PREFIX}/share/tamper/src/
+
+ls -lah ${PREFIX}/share/tamper/src/
+
+#Adding python executable for the script to work
+echo "#!/bin/bash" > ${PREFIX}/bin/predict_tAMPer
+echo "python ${PREFIX}/share/tamper/src/predict_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/predict_tAMPer
+
+echo "#!/bin/bash" > ${PREFIX}/bin/train_tAMPer.py
+echo "python ${PREFIX}/share/tamper/src/train_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/train_tAMPer
+
+#Checking if files are copied within bin
+echo "Files in ${PREFIX}/bin/:"
+ls -l ${PREFIX}/bin/
+
+chmod +x ${PREFIX}/bin/predict_tAMPer
+chmod +x ${PREFIX}/bin/train_tAMPer
+
+#Verify permissions
+echo "Permissions after chmod:"
+ls -l ${PREFIX}/share/tamper/src/
diff --git a/recipes/tamper/meta.yaml b/recipes/tamper/meta.yaml
new file mode 100644
index 0000000000000..115cc7d22b98f
--- /dev/null
+++ b/recipes/tamper/meta.yaml
@@ -0,0 +1,47 @@
+{% set name = "tamper" %}
+{% set version = "1.0.1" %}
+
+package:
+  name: '{{ name|lower }}'
+  version: '{{ version }}'
+
+source:
+  url: https://github.com/bcgsc/tAMPer/releases/download/v{{ version }}/tAMPer_v{{ version }}.tar.gz
+  sha256: 0c4cfc57a844b89dbc9c020084b5d12b096359a7341350552f5ea707d882486a
+
+build:
+  number: 1
+  noarch: generic
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x.x') }}
+
+requirements:
+  host:
+    - python >=3.9
+  run:
+    - biopython=1.79
+    - fair-esm=2.0.0
+    - libboost=1.73.0
+    - loguru=0.7.0
+    - matplotlib=3.8.4       
+    - numpy=1.24.3
+    - pandas=1.5.3
+    - pytorch=1.13.1
+    - pytorch_cluster=1.6.1
+    - pytorch_geometric=2.3.0
+    - torch-scatter=2.1.1
+    - transformers=4.41.2
+    - scikit-learn=1.2.2
+    - scipy=1.10.1
+
+test:
+  commands:
+    - train_tAMPer -h
+    - predict_tAMPer -h
+
+about:
+  home: https://github.com/bcgsc/tAMPer
+  license: GPL-3
+  license_family: GPL
+  license_file: LICENSE
+  summary: Structure-aware deep learning model for peptides toxicity prediction
\ No newline at end of file

From 045e865e488f347f64d06c14db4341590209ba42 Mon Sep 17 00:00:00 2001
From: berkeucar <bucar.cs@gmail.com>
Date: Thu, 19 Sep 2024 11:23:19 -0700
Subject: [PATCH 08/13] made name consistent with the version

---
 recipes/dssp/meta.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/recipes/dssp/meta.yaml b/recipes/dssp/meta.yaml
index ec9d72728cf70..58841bd18016d 100644
--- a/recipes/dssp/meta.yaml
+++ b/recipes/dssp/meta.yaml
@@ -1,7 +1,8 @@
 {% set version = "3.0.0" %}
+{% set name = "dssp"}
 # This file, the patch file and build file were taken from conda salilab channel's recipes - please see https://github.com/salilab/conda-recipes for more.
 package:
-  name: dssp
+  name: {{ name }}
   version: {{ version }}
 
 source:

From da6359cccce66e5c7324de0edec14067eb8cba73 Mon Sep 17 00:00:00 2001
From: berkeucar <bucar.cs@gmail.com>
Date: Thu, 19 Sep 2024 11:34:18 -0700
Subject: [PATCH 09/13] deleted tamper

---
 recipes/tamper/build.sh  | 33 ----------------------------
 recipes/tamper/meta.yaml | 47 ----------------------------------------
 2 files changed, 80 deletions(-)
 delete mode 100644 recipes/tamper/build.sh
 delete mode 100644 recipes/tamper/meta.yaml

diff --git a/recipes/tamper/build.sh b/recipes/tamper/build.sh
deleted file mode 100644
index 0c87f849ba1e0..0000000000000
--- a/recipes/tamper/build.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/bash
-
-mkdir -p ${PREFIX}/bin/
-mkdir -p ${PREFIX}/share/tamper/
-mkdir -p ${PREFIX}/share/tamper/src/
-mkdir -p ${PREFIX}/share/tamper/checkpoints/trained
-cp -r src/. ${PREFIX}/share/tamper/src/
-cp -r checkpoints/trained/. ${PREFIX}/share/tamper/checkpoints/trained
-ls ${PREFIX}/share/tamper/src/
-
-#This allows src code to be executbale for user and group
-chmod -R u+x ${PREFIX}/share/tamper/src/
-chmod -R g+x ${PREFIX}/share/tamper/src/
-
-ls -lah ${PREFIX}/share/tamper/src/
-
-#Adding python executable for the script to work
-echo "#!/bin/bash" > ${PREFIX}/bin/predict_tAMPer
-echo "python ${PREFIX}/share/tamper/src/predict_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/predict_tAMPer
-
-echo "#!/bin/bash" > ${PREFIX}/bin/train_tAMPer.py
-echo "python ${PREFIX}/share/tamper/src/train_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/train_tAMPer
-
-#Checking if files are copied within bin
-echo "Files in ${PREFIX}/bin/:"
-ls -l ${PREFIX}/bin/
-
-chmod +x ${PREFIX}/bin/predict_tAMPer
-chmod +x ${PREFIX}/bin/train_tAMPer
-
-#Verify permissions
-echo "Permissions after chmod:"
-ls -l ${PREFIX}/share/tamper/src/
diff --git a/recipes/tamper/meta.yaml b/recipes/tamper/meta.yaml
deleted file mode 100644
index 115cc7d22b98f..0000000000000
--- a/recipes/tamper/meta.yaml
+++ /dev/null
@@ -1,47 +0,0 @@
-{% set name = "tamper" %}
-{% set version = "1.0.1" %}
-
-package:
-  name: '{{ name|lower }}'
-  version: '{{ version }}'
-
-source:
-  url: https://github.com/bcgsc/tAMPer/releases/download/v{{ version }}/tAMPer_v{{ version }}.tar.gz
-  sha256: 0c4cfc57a844b89dbc9c020084b5d12b096359a7341350552f5ea707d882486a
-
-build:
-  number: 1
-  noarch: generic
-  run_exports:
-    - {{ pin_subpackage(name, max_pin='x.x') }}
-
-requirements:
-  host:
-    - python >=3.9
-  run:
-    - biopython=1.79
-    - fair-esm=2.0.0
-    - libboost=1.73.0
-    - loguru=0.7.0
-    - matplotlib=3.8.4       
-    - numpy=1.24.3
-    - pandas=1.5.3
-    - pytorch=1.13.1
-    - pytorch_cluster=1.6.1
-    - pytorch_geometric=2.3.0
-    - torch-scatter=2.1.1
-    - transformers=4.41.2
-    - scikit-learn=1.2.2
-    - scipy=1.10.1
-
-test:
-  commands:
-    - train_tAMPer -h
-    - predict_tAMPer -h
-
-about:
-  home: https://github.com/bcgsc/tAMPer
-  license: GPL-3
-  license_family: GPL
-  license_file: LICENSE
-  summary: Structure-aware deep learning model for peptides toxicity prediction
\ No newline at end of file

From 7063601832737f07c6a014680fc6bc31bd391aae Mon Sep 17 00:00:00 2001
From: berkeucar <bucar.cs@gmail.com>
Date: Thu, 19 Sep 2024 12:00:29 -0700
Subject: [PATCH 10/13] fixed the mistake for the dssp name

---
 recipes/dssp/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/dssp/meta.yaml b/recipes/dssp/meta.yaml
index 58841bd18016d..36d27564196c3 100644
--- a/recipes/dssp/meta.yaml
+++ b/recipes/dssp/meta.yaml
@@ -1,5 +1,5 @@
 {% set version = "3.0.0" %}
-{% set name = "dssp"}
+{% set name = "dssp" %}
 # This file, the patch file and build file were taken from conda salilab channel's recipes - please see https://github.com/salilab/conda-recipes for more.
 package:
   name: {{ name }}

From ceca771fdcb71f494a16eac67936058c8d6d7647 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Berke=20U=C3=A7ar?=
 <63494583+berkeucar@users.noreply.github.com>
Date: Fri, 20 Sep 2024 10:05:20 -0700
Subject: [PATCH 11/13] Update recipes/dssp/build.sh

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>
---
 recipes/dssp/build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/dssp/build.sh b/recipes/dssp/build.sh
index 2316905bb2de1..d774cf96670be 100644
--- a/recipes/dssp/build.sh
+++ b/recipes/dssp/build.sh
@@ -20,4 +20,4 @@ if [ `uname -s` = "Darwin" ]; then
   CFLAGS="-std=c++11 -Wno-enum-constexpr-conversion ${CFLAGS}"
 fi
 
-make -j4 install
+make -j${CPU_COUNT} install

From b924d1b19dd9dc11ffc346f9eb56c8f6dc449568 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Berke=20U=C3=A7ar?=
 <63494583+berkeucar@users.noreply.github.com>
Date: Fri, 20 Sep 2024 10:05:26 -0700
Subject: [PATCH 12/13] Update recipes/dssp/meta.yaml

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>
---
 recipes/dssp/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/dssp/meta.yaml b/recipes/dssp/meta.yaml
index 36d27564196c3..527a024ebe133 100644
--- a/recipes/dssp/meta.yaml
+++ b/recipes/dssp/meta.yaml
@@ -6,7 +6,7 @@ package:
   version: {{ version }}
 
 source:
-  url: https://salilab.org/dssp/dssp-3.0.0.tgz
+  url: https://salilab.org/dssp/dssp-{{ version }}.tgz
   sha256: 25d39a2107767b622a59dd9fa790112c1516564b8518fc6ac0fab081d5ac3ab0
   patches:
     - dssp-boost-tr1.patch #Rebuild with latest gcc and boost - this was taken from the 

From c81df5da55f20128536291b803d44842ea151e7d Mon Sep 17 00:00:00 2001
From: berkeucar <bucar.cs@gmail.com>
Date: Wed, 6 Nov 2024 17:04:29 -0800
Subject: [PATCH 13/13] added tamper

---
 recipes/tamper/build.sh  | 34 +++++++++++++++++++++++++++++++
 recipes/tamper/meta.yaml | 43 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 77 insertions(+)
 create mode 100755 recipes/tamper/build.sh
 create mode 100644 recipes/tamper/meta.yaml

diff --git a/recipes/tamper/build.sh b/recipes/tamper/build.sh
new file mode 100755
index 0000000000000..7cd4ed88cc919
--- /dev/null
+++ b/recipes/tamper/build.sh
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+mkdir -p ${PREFIX}/bin/
+mkdir -p ${PREFIX}/share/tamper/
+mkdir -p ${PREFIX}/share/tamper/src/
+mkdir -p ${PREFIX}/share/tamper/checkpoints/trained
+cp -r src/. ${PREFIX}/share/tamper/src/
+cp -r checkpoints/trained/. ${PREFIX}/share/tamper/checkpoints/trained
+ls ${PREFIX}/share/tamper/src/
+
+#This allows src code to be executbale for user and group
+chmod -R u+x ${PREFIX}/share/tamper/src/
+chmod -R g+x ${PREFIX}/share/tamper/src/
+
+ls -lah ${PREFIX}/share/tamper/src/
+
+#Adding python executable for the script to work
+echo "#!/bin/bash" > ${PREFIX}/bin/predict_tAMPer
+echo "python ${PREFIX}/share/tamper/src/predict_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/predict_tAMPer
+
+echo "#!/bin/bash" > ${PREFIX}/bin/train_tAMPer.py
+echo "python ${PREFIX}/share/tamper/src/train_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/train_tAMPer
+
+#Checking if files are copied within bin
+echo "Files in ${PREFIX}/bin/:"
+ls -l ${PREFIX}/bin/
+
+chmod +x ${PREFIX}/bin/predict_tAMPer
+chmod +x ${PREFIX}/bin/train_tAMPer
+
+#Verify permissions
+echo "Permissions after chmod:"
+ls -l ${PREFIX}/share/tamper/src/
+
diff --git a/recipes/tamper/meta.yaml b/recipes/tamper/meta.yaml
new file mode 100644
index 0000000000000..46966f2d5f401
--- /dev/null
+++ b/recipes/tamper/meta.yaml
@@ -0,0 +1,43 @@
+{% set name = "tamper" %}
+{% set version = "1.0.1" %}
+
+package:
+  name: '{{ name|lower }}'
+  version: '{{ version }}'
+
+source:
+  url: https://github.com/bcgsc/tAMPer/releases/download/v{{ version }}/tAMPer_v{{ version }}.tar.gz
+  sha256: 0c4cfc57a844b89dbc9c020084b5d12b096359a7341350552f5ea707d882486a
+
+build:
+  number: 1
+  noarch: generic
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x.x') }}
+
+requirements:
+  host:
+    - python >=3.9
+  run:
+    - biopython
+    - dssp
+    - fair-esm>=2.0.0
+    - loguru
+    - pandas
+    - python>=3.9
+    - pytorch
+    - pytorch_cluster
+    - pytorch_geometric
+    - torch-scatter
+
+test:
+  commands:
+    - train_tAMPer -h
+    - predict_tAMPer -h
+
+about:
+  home: https://github.com/bcgsc/tAMPer
+  license: GPL-3
+  license_family: GPL
+  license_file: LICENSE
+  summary: Structure-aware deep learning model for peptides toxicity prediction