From 972d04fb9583794f36d2128d58400554f8bfd9de Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 9 Oct 2023 07:18:26 +0000
Subject: [PATCH 01/12] {2023.06}[gompi/2022a] HISAT2 V2.2.1

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index 142acbec8f..6ebc555948 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -49,3 +49,4 @@ easyconfigs:
   - NLopt-2.7.1-GCCcore-11.3.0.eb
   - PCRE2-10.40-GCCcore-11.3.0.eb
   - Tk-8.6.12-GCCcore-11.3.0.eb
+  - HISAT2-2.2.1-gompi-2022a.eb

From 879361afdff1c60e10cd9fd9c29390337c420c13 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Wed, 10 Jan 2024 14:22:00 +0100
Subject: [PATCH 02/12] Update configure_easybuild

Exception for Saga
---
 configure_easybuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/configure_easybuild b/configure_easybuild
index 7dca1ce682..5465ce1e6a 100644
--- a/configure_easybuild
+++ b/configure_easybuild
@@ -1,6 +1,6 @@
 export EASYBUILD_PREFIX=${WORKDIR}/easybuild
 export EASYBUILD_INSTALLPATH=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR}
-export EASYBUILD_SOURCEPATH=${WORKDIR}/easybuild/sources:${EESSI_SOURCEPATH}
+export EASYBUILD_SOURCEPATH=${WORKDIR}/easybuild/sources:${EESSI_SOURCEPATH}:/cluster/projects/nn9992k/pilot.nessi.no/sources/
 
 # just ignore OS dependencies for now, see https://github.com/easybuilders/easybuild-framework/issues/3430
 export EASYBUILD_IGNORE_OSDEPS=1

From ce65b9964251cf258f8e1231505dea4dff217f50 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Wed, 10 Jan 2024 17:52:37 +0100
Subject: [PATCH 03/12] Update configure_easybuild

Default
---
 configure_easybuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/configure_easybuild b/configure_easybuild
index 5465ce1e6a..7dca1ce682 100644
--- a/configure_easybuild
+++ b/configure_easybuild
@@ -1,6 +1,6 @@
 export EASYBUILD_PREFIX=${WORKDIR}/easybuild
 export EASYBUILD_INSTALLPATH=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR}
-export EASYBUILD_SOURCEPATH=${WORKDIR}/easybuild/sources:${EESSI_SOURCEPATH}:/cluster/projects/nn9992k/pilot.nessi.no/sources/
+export EASYBUILD_SOURCEPATH=${WORKDIR}/easybuild/sources:${EESSI_SOURCEPATH}
 
 # just ignore OS dependencies for now, see https://github.com/easybuilders/easybuild-framework/issues/3430
 export EASYBUILD_IGNORE_OSDEPS=1

From 5cee43332a2dad6b1311c15922a7a5249155fbe3 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Wed, 10 Jan 2024 17:56:51 +0100
Subject: [PATCH 04/12] Create file-5.43-GCCcore-11.3.0.eb

Added the easyconfig with the change of protocol
---
 file-5.43-GCCcore-11.3.0.eb | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 file-5.43-GCCcore-11.3.0.eb

diff --git a/file-5.43-GCCcore-11.3.0.eb b/file-5.43-GCCcore-11.3.0.eb
new file mode 100644
index 0000000000..1128c37d6a
--- /dev/null
+++ b/file-5.43-GCCcore-11.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'file'
+version = '5.43'
+
+homepage = 'https://www.darwinsys.com/file/'
+description = """The file command is 'a file type guesser', that is, a command-line tool
+ that tells you in words what kind of data a file contains."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['ftp://ftp.astron.com/pub/file/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['8c8015e91ae0e8d0321d94c78239892ef9dbc70c4ade0008c0e95894abfb1991']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('binutils', '2.38'),
+]
+
+preconfigopts = "autoreconf -f -i && "
+
+sanity_check_paths = {
+    'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT],
+    'dirs': ['share']
+}
+
+moduleclass = 'system'

From 72e0e8c98257a207eed302601b54398450767712 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Wed, 10 Jan 2024 17:58:30 +0100
Subject: [PATCH 05/12] Update file-5.43-GCCcore-11.3.0.eb

Change the download protocol
---
 file-5.43-GCCcore-11.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/file-5.43-GCCcore-11.3.0.eb b/file-5.43-GCCcore-11.3.0.eb
index 1128c37d6a..9c5e9a2b84 100644
--- a/file-5.43-GCCcore-11.3.0.eb
+++ b/file-5.43-GCCcore-11.3.0.eb
@@ -9,7 +9,7 @@ description = """The file command is 'a file type guesser', that is, a command-l
 
 toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
-source_urls = ['ftp://ftp.astron.com/pub/file/']
+source_urls = ['http://ftp.astron.com/pub/file/']
 sources = [SOURCE_TAR_GZ]
 checksums = ['8c8015e91ae0e8d0321d94c78239892ef9dbc70c4ade0008c0e95894abfb1991']
 

From dfa5ed502382bd9fc226967a487e082b03d41aa2 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Wed, 10 Jan 2024 18:25:28 +0100
Subject: [PATCH 06/12] Update EESSI-pilot-install-software.sh

Trying to install the file package within EESSI-pilot-software.sh
---
 EESSI-pilot-install-software.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh
index 026919157f..f97e57c576 100755
--- a/EESSI-pilot-install-software.sh
+++ b/EESSI-pilot-install-software.sh
@@ -226,6 +226,7 @@ for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[
 done
 
 ### add packages here
+${EB} --easystack ${TOPDIR}/file-5.43-GCCcore-11.3.0.eb --robot
 
 echo ">> Creating/updating Lmod cache..."
 export LMOD_RC="${EASYBUILD_INSTALLPATH}/.lmod/lmodrc.lua"

From 6850031b89c1a465495d2364e9c1321599867733 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Wed, 10 Jan 2024 18:28:24 +0100
Subject: [PATCH 07/12] Update EESSI-pilot-install-software.sh

---
 EESSI-pilot-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh
index f97e57c576..e90e6f8f40 100755
--- a/EESSI-pilot-install-software.sh
+++ b/EESSI-pilot-install-software.sh
@@ -226,7 +226,7 @@ for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[
 done
 
 ### add packages here
-${EB} --easystack ${TOPDIR}/file-5.43-GCCcore-11.3.0.eb --robot
+${EB}  ${TOPDIR}/file-5.43-GCCcore-11.3.0.eb --robot
 
 echo ">> Creating/updating Lmod cache..."
 export LMOD_RC="${EASYBUILD_INSTALLPATH}/.lmod/lmodrc.lua"

From 424d60dc5ed5b9adc306d86716098a4a6c627249 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Wed, 10 Jan 2024 18:48:15 +0100
Subject: [PATCH 08/12] Update EESSI-pilot-install-software.sh

The file must be installed before the easystack_file check
---
 EESSI-pilot-install-software.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh
index e90e6f8f40..9dae9f2ae7 100755
--- a/EESSI-pilot-install-software.sh
+++ b/EESSI-pilot-install-software.sh
@@ -201,6 +201,8 @@ for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[
     ${EB} --show-config
 
     echo_green "All set, let's start installing some software with EasyBuild v${eb_version} in ${EASYBUILD_INSTALLPATH}..."
+    
+    ${EB}  ${TOPDIR}/file-5.43-GCCcore-11.3.0.eb --robot
 
     if [ -f ${easystack_file} ]; then
         echo_green "Feeding easystack file ${easystack_file} to EasyBuild..."
@@ -226,7 +228,7 @@ for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[
 done
 
 ### add packages here
-${EB}  ${TOPDIR}/file-5.43-GCCcore-11.3.0.eb --robot
+
 
 echo ">> Creating/updating Lmod cache..."
 export LMOD_RC="${EASYBUILD_INSTALLPATH}/.lmod/lmodrc.lua"

From aba11b25d1483cf6110d3eb3a6b7db079033bba2 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Wed, 10 Jan 2024 21:05:21 +0100
Subject: [PATCH 09/12] Delete file-5.43-GCCcore-11.3.0.eb

Revert Changes
---
 file-5.43-GCCcore-11.3.0.eb | 28 ----------------------------
 1 file changed, 28 deletions(-)
 delete mode 100644 file-5.43-GCCcore-11.3.0.eb

diff --git a/file-5.43-GCCcore-11.3.0.eb b/file-5.43-GCCcore-11.3.0.eb
deleted file mode 100644
index 9c5e9a2b84..0000000000
--- a/file-5.43-GCCcore-11.3.0.eb
+++ /dev/null
@@ -1,28 +0,0 @@
-easyblock = 'ConfigureMake'
-
-name = 'file'
-version = '5.43'
-
-homepage = 'https://www.darwinsys.com/file/'
-description = """The file command is 'a file type guesser', that is, a command-line tool
- that tells you in words what kind of data a file contains."""
-
-toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
-
-source_urls = ['http://ftp.astron.com/pub/file/']
-sources = [SOURCE_TAR_GZ]
-checksums = ['8c8015e91ae0e8d0321d94c78239892ef9dbc70c4ade0008c0e95894abfb1991']
-
-builddependencies = [
-    ('Autotools', '20220317'),
-    ('binutils', '2.38'),
-]
-
-preconfigopts = "autoreconf -f -i && "
-
-sanity_check_paths = {
-    'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT],
-    'dirs': ['share']
-}
-
-moduleclass = 'system'

From 3385bf391364a931117375f580207f4a1773c4d5 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Wed, 10 Jan 2024 21:06:23 +0100
Subject: [PATCH 10/12] Update EESSI-pilot-install-software.sh

Revert Changes
---
 EESSI-pilot-install-software.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh
index 9dae9f2ae7..53b51d2f90 100755
--- a/EESSI-pilot-install-software.sh
+++ b/EESSI-pilot-install-software.sh
@@ -202,8 +202,6 @@ for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[
 
     echo_green "All set, let's start installing some software with EasyBuild v${eb_version} in ${EASYBUILD_INSTALLPATH}..."
     
-    ${EB}  ${TOPDIR}/file-5.43-GCCcore-11.3.0.eb --robot
-
     if [ -f ${easystack_file} ]; then
         echo_green "Feeding easystack file ${easystack_file} to EasyBuild..."
 

From a34a595164ea6a20062e86567de1311cb08ec35b Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Wed, 10 Jan 2024 21:09:58 +0100
Subject: [PATCH 11/12] Update EESSI-pilot-install-software.sh

Revert Changes
---
 EESSI-pilot-install-software.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh
index 53b51d2f90..9e4c47b94b 100755
--- a/EESSI-pilot-install-software.sh
+++ b/EESSI-pilot-install-software.sh
@@ -227,7 +227,6 @@ done
 
 ### add packages here
 
-
 echo ">> Creating/updating Lmod cache..."
 export LMOD_RC="${EASYBUILD_INSTALLPATH}/.lmod/lmodrc.lua"
 if [ ! -f $LMOD_RC ]; then

From ef1ae88a36eaf17869e07d6944c4f26482c9347a Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Thu, 11 Jan 2024 10:08:20 +0100
Subject: [PATCH 12/12] Update EESSI-pilot-install-software.sh

---
 EESSI-pilot-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh
index 9e4c47b94b..026919157f 100755
--- a/EESSI-pilot-install-software.sh
+++ b/EESSI-pilot-install-software.sh
@@ -201,7 +201,7 @@ for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[
     ${EB} --show-config
 
     echo_green "All set, let's start installing some software with EasyBuild v${eb_version} in ${EASYBUILD_INSTALLPATH}..."
-    
+
     if [ -f ${easystack_file} ]; then
         echo_green "Feeding easystack file ${easystack_file} to EasyBuild..."