From 740d5cb4aee63137ea867e846bfd02c52a8b3dbf Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 17:00:54 +0100 Subject: [PATCH 01/19] test --- trombinoscope/staff/valentin-guignon2.yaml | 48 ++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 trombinoscope/staff/valentin-guignon2.yaml diff --git a/trombinoscope/staff/valentin-guignon2.yaml b/trombinoscope/staff/valentin-guignon2.yaml new file mode 100644 index 0000000..ed73e6a --- /dev/null +++ b/trombinoscope/staff/valentin-guignon2.yaml @@ -0,0 +1,48 @@ +--- +staffname: Valentin Guignon +type: staff +active: true +email: v.guignon@cgiar.org +phone: 0434352433 ext. 204 +city: + - Montpellier +workplace: Alliance Bioversity and CIAT +affiliation: Bioversity International - UMR AGAP +facility: SouthGreen +category: +- software +- development +- genomics +homepage: https://fr.linkedin.com/in/valentin-guignon +orcid: 0000-0003-0903-6811 +image: valentin-guignon.jpg +keywords: + - BrAPI + - Gigwa + - MGIS + - Genome Hubs + - GreenPhyl + - Banana + - Orthology + - Gene families + - Interoperability + - Git + - Tripal + - Drupal + - CMS + - PostgreSQL + - PHP + - Javascript + - Perl + - Python + - Java + - nodejs + - algorithm + - pipeline +role: Bioinformatician +bio: + I work at The Alliance (CGIAR) as associate scientist on multiple projects + (BrAPI, Gigwa, MGIS, Banana Genome Hub, GenoRing, GreenPhyl, Tripal,...). I am + currently part of the Tripal Advisory Committee and the BrAPI Advisory Board. + I have strong knowledge in databases and web development with an expertise on + the Drupal CMS. I design algorithms, methodologies and software. \ No newline at end of file From 0118098049de8f810cac727efa2f164a1faf3127 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 17:09:55 +0100 Subject: [PATCH 02/19] change path to check yaml --- .github/workflows/check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 22ba276..4728a1d 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -3,7 +3,7 @@ name: check on: push: paths: - - "staff/**.yaml" + - "trombinoscope/staff/**.yaml" concurrency: group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} From cd70ee14bcd1e3fb6d47f45f204b4d9e41f3fff4 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 17:32:59 +0100 Subject: [PATCH 03/19] Update check.yaml --- .github/workflows/check.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 4728a1d..c780a95 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -1,9 +1,9 @@ name: check -on: - push: - paths: - - "trombinoscope/staff/**.yaml" +#on: +# push: +# paths: +# - "trombinoscope/staff/**.yaml" concurrency: group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} From bbf1903c8bf3c730b9710aea6796f281c60097e2 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 17:35:39 +0100 Subject: [PATCH 04/19] Update check.yaml --- .github/workflows/check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index c780a95..4ca31aa 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -1,6 +1,6 @@ name: check -#on: +on: push # push: # paths: # - "trombinoscope/staff/**.yaml" From a137ea910a42feb54921f29cdcccecac0d30acce Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 17:37:48 +0100 Subject: [PATCH 05/19] Update check.yaml --- .github/workflows/check.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 4ca31aa..6293fe9 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -1,9 +1,9 @@ name: check -on: push -# push: -# paths: -# - "trombinoscope/staff/**.yaml" +on: + push: + paths: + - "trombinoscope/staff/**" concurrency: group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} From c1b208e4e9ba57f707f3d0f53f69241908868cf3 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 17:38:14 +0100 Subject: [PATCH 06/19] Update valentin-guignon2.yaml --- trombinoscope/staff/valentin-guignon2.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/trombinoscope/staff/valentin-guignon2.yaml b/trombinoscope/staff/valentin-guignon2.yaml index ed73e6a..79f7e08 100644 --- a/trombinoscope/staff/valentin-guignon2.yaml +++ b/trombinoscope/staff/valentin-guignon2.yaml @@ -8,7 +8,7 @@ city: - Montpellier workplace: Alliance Bioversity and CIAT affiliation: Bioversity International - UMR AGAP -facility: SouthGreen +facility: SouthGreenn category: - software - development @@ -45,4 +45,4 @@ bio: (BrAPI, Gigwa, MGIS, Banana Genome Hub, GenoRing, GreenPhyl, Tripal,...). I am currently part of the Tripal Advisory Committee and the BrAPI Advisory Board. I have strong knowledge in databases and web development with an expertise on - the Drupal CMS. I design algorithms, methodologies and software. \ No newline at end of file + the Drupal CMS. I design algorithms, methodologies and software. From 5280a3b2d6cf006e9c78baf0fe81a3b8379627f2 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 17:43:08 +0100 Subject: [PATCH 07/19] Update build.yaml --- .github/workflows/build.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index e4d2b0d..c0d2523 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -17,6 +17,7 @@ concurrency: jobs: build: + if: ${{ github.event.workflow_run.conclusion == 'success' }} runs-on: ubuntu-22.04 steps: From 9ea951aa35ac2643046bc036087185032369cd6a Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 17:44:35 +0100 Subject: [PATCH 08/19] Update check.yaml --- .github/workflows/check.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 6293fe9..8ff783a 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -1,9 +1,9 @@ name: check -on: - push: - paths: - - "trombinoscope/staff/**" +on: push +# push: +# paths: +# - "trombinoscope/staff/**" concurrency: group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} From efabd857a35eb76d220e8a858a3f25226e10ee78 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 19:04:40 +0100 Subject: [PATCH 09/19] Delete trombinoscope/staff/valentin-guignon2.yaml --- trombinoscope/staff/valentin-guignon2.yaml | 48 ---------------------- 1 file changed, 48 deletions(-) delete mode 100644 trombinoscope/staff/valentin-guignon2.yaml diff --git a/trombinoscope/staff/valentin-guignon2.yaml b/trombinoscope/staff/valentin-guignon2.yaml deleted file mode 100644 index 79f7e08..0000000 --- a/trombinoscope/staff/valentin-guignon2.yaml +++ /dev/null @@ -1,48 +0,0 @@ ---- -staffname: Valentin Guignon -type: staff -active: true -email: v.guignon@cgiar.org -phone: 0434352433 ext. 204 -city: - - Montpellier -workplace: Alliance Bioversity and CIAT -affiliation: Bioversity International - UMR AGAP -facility: SouthGreenn -category: -- software -- development -- genomics -homepage: https://fr.linkedin.com/in/valentin-guignon -orcid: 0000-0003-0903-6811 -image: valentin-guignon.jpg -keywords: - - BrAPI - - Gigwa - - MGIS - - Genome Hubs - - GreenPhyl - - Banana - - Orthology - - Gene families - - Interoperability - - Git - - Tripal - - Drupal - - CMS - - PostgreSQL - - PHP - - Javascript - - Perl - - Python - - Java - - nodejs - - algorithm - - pipeline -role: Bioinformatician -bio: - I work at The Alliance (CGIAR) as associate scientist on multiple projects - (BrAPI, Gigwa, MGIS, Banana Genome Hub, GenoRing, GreenPhyl, Tripal,...). I am - currently part of the Tripal Advisory Committee and the BrAPI Advisory Board. - I have strong knowledge in databases and web development with an expertise on - the Drupal CMS. I design algorithms, methodologies and software. From 8e95225be1a64534dff101c84154fedc349ad74c Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 19:26:32 +0100 Subject: [PATCH 10/19] fix path photo --- trombinoscope/staff/gaetan-droc.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/trombinoscope/staff/gaetan-droc.yaml b/trombinoscope/staff/gaetan-droc.yaml index a32e822..bda340a 100644 --- a/trombinoscope/staff/gaetan-droc.yaml +++ b/trombinoscope/staff/gaetan-droc.yaml @@ -30,7 +30,7 @@ bibtex: gaetan-droc.bib orcid: 0000-0003-1849-1269 -image: gaetan-droc.png +image: gaetan-droc.jpg keywords: - genome annotation From e96784821c3a23da25e37b1ea0fef6f4958310a8 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 19:52:59 +0100 Subject: [PATCH 11/19] fix url validation --- .github/workflows/check_scripts/check_yaml.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/.github/workflows/check_scripts/check_yaml.py b/.github/workflows/check_scripts/check_yaml.py index 5b1d935..1d0ba26 100755 --- a/.github/workflows/check_scripts/check_yaml.py +++ b/.github/workflows/check_scripts/check_yaml.py @@ -15,7 +15,6 @@ def validate_category(d,f): def check_bibtex_file(d, f): p = pathlib.Path(f).parent.parent / 'publication' - print(p) if 'bibtex' in d and d['bibtex']: return (p / d['bibtex']).exists() return True @@ -31,12 +30,17 @@ def validate_orcid(d, f): def validate_url(d, f): regex = re.compile(r'^https?://') - try: - if re.search(regex, d['homepage']): - return False - except Exception: + if 'homepage' in d.keys(): + if d['homepage'] is not None: + if re.search(regex, d['homepage']): + return True + else: # case value do not follow specification + return False + else: # case no value provided for homepage tag + return True + else: # case no homepage tag return True - return True + From 9e529c0fdeba51754af493e666a9b2b3fb6215f9 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 20:13:08 +0100 Subject: [PATCH 12/19] fix test path qhen non printable chracter exists --- .github/workflows/check_scripts/images_exist.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/check_scripts/images_exist.sh b/.github/workflows/check_scripts/images_exist.sh index d162cb9..4c5fbb0 100755 --- a/.github/workflows/check_scripts/images_exist.sh +++ b/.github/workflows/check_scripts/images_exist.sh @@ -12,9 +12,9 @@ awk '/^[[:blank:]]*image: / { if [[ $ymlfile == *TEMPLATE* ]]; then continue fi + imgfile=$(tr -dc '[[:print:]]' <<< "$imgfile") # remove non printable character if [ ! -e "$imgfile" ]; then - printf '%s (from %s) does not exist\n' \ - "$imgfile" "$ymlfile" >&2 + echo "Achtung: $imgfile (from $ymlfile) does not exist\n" >&2 success=false fi done From bb9d53f14fc8672fe72d4ec851d8cc312726c13a Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 20:27:43 +0100 Subject: [PATCH 13/19] fix yaml --- trombinoscope/staff/jacques-dainat.yaml | 2 +- trombinoscope/staff/pierre-larmande.yaml | 28 ++++++++++++----------- trombinoscope/staff/valentin-guignon.yaml | 9 ++++---- 3 files changed, 21 insertions(+), 18 deletions(-) diff --git a/trombinoscope/staff/jacques-dainat.yaml b/trombinoscope/staff/jacques-dainat.yaml index 6c6b762..4912a5b 100644 --- a/trombinoscope/staff/jacques-dainat.yaml +++ b/trombinoscope/staff/jacques-dainat.yaml @@ -28,6 +28,6 @@ category: phone: +33 (0)00 00 00 00 city: - Montpellier -affiliation: IRD-UM-CNRS +affiliation: IRD workplace: IRD facility: SouthGreen diff --git a/trombinoscope/staff/pierre-larmande.yaml b/trombinoscope/staff/pierre-larmande.yaml index 132d3b7..4a1fcf7 100644 --- a/trombinoscope/staff/pierre-larmande.yaml +++ b/trombinoscope/staff/pierre-larmande.yaml @@ -49,7 +49,7 @@ facility: SouthGreen # category: - development - - annotation + - annotation - dataservices - systems biology # @@ -64,7 +64,7 @@ bibtex: pierre-larmande.bib # # If you have an ORCID ID ("NNNN-NNNN-NNNN-NNNN") # -orcid: 0000-0002-2923-9790 +orcid: 0000-0002-2923-9790 # # The name of an image file in the "img" subdirectory, no more than # about 400 pixels wide and less than 200 KB in file size. @@ -84,16 +84,18 @@ keywords: # # "role:" is the role that you play within your infrastructure. # -role: Researcher +role: Researcher # bio: - Pierre Larmande is senior researcher at IRD, the French Public Research Institute for Sustainable Development. He is member of the DIADE Unit in Montpellier. His main research interests are Data integration, Semantic Web, plant-ontologies, semantic data linking, Knowledge management and Big Data for plant genomics. - - - He obtained PhD in Informatics from the university of Montpellier in 2007 (about federated plant data integration approaches applied to agronomy) and recently obtained the habilitation to conduct research supervision (HDR) in 2020. He coordinated the Oryza Tag Line phenotypic rice mutant database and was involved in the OrygenesDB T-DNA rice database. - - - Pierre Larmande is the lead PI of the Agronomic Linked Data project (AgroLD), which is a Knowledge Graph database that consists of data integrated from a variety of plant resources and ontologies. - - - + Pierre Larmande is senior researcher at IRD, the French Public Research + Institute for Sustainable Development. He is member of the DIADE Unit in + Montpellier. His main research interests are Data integration, Semantic Web, + plant-ontologies, semantic data linking, Knowledge management and Big Data + for plant genomics. He obtained PhD in Informatics from the university of + Montpellier in 2007 (about federated plant data integration approaches + applied to agronomy) and recently obtained the habilitation to conduct + research supervision (HDR) in 2020. He coordinated the Oryza Tag Line + phenotypic rice mutant database and was involved in the OrygenesDB T-DNA rice + database. Pierre Larmande is the lead PI of the Agronomic Linked Data project + (AgroLD), which is a Knowledge Graph database that consists of data + integrated from a variety of plant resources and ontologies. diff --git a/trombinoscope/staff/valentin-guignon.yaml b/trombinoscope/staff/valentin-guignon.yaml index ed73e6a..a11836a 100644 --- a/trombinoscope/staff/valentin-guignon.yaml +++ b/trombinoscope/staff/valentin-guignon.yaml @@ -10,9 +10,9 @@ workplace: Alliance Bioversity and CIAT affiliation: Bioversity International - UMR AGAP facility: SouthGreen category: -- software -- development -- genomics + - software + - development + - genomics homepage: https://fr.linkedin.com/in/valentin-guignon orcid: 0000-0003-0903-6811 image: valentin-guignon.jpg @@ -45,4 +45,5 @@ bio: (BrAPI, Gigwa, MGIS, Banana Genome Hub, GenoRing, GreenPhyl, Tripal,...). I am currently part of the Tripal Advisory Committee and the BrAPI Advisory Board. I have strong knowledge in databases and web development with an expertise on - the Drupal CMS. I design algorithms, methodologies and software. \ No newline at end of file + the Drupal CMS. I design algorithms, methodologies and software. + \ No newline at end of file From 96ff9cd7a55a0a5f496900da5338306cf1cb42b0 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 20:32:38 +0100 Subject: [PATCH 14/19] fix yaml --- trombinoscope/staff/TEMPLATE.yaml | 2 +- trombinoscope/staff/alexis-dereeper.yaml | 6 +++--- trombinoscope/staff/gaetan-droc.yaml | 5 ++--- trombinoscope/staff/mathieu-rouard.yaml | 8 ++++---- trombinoscope/staff/pierre-larmande.yaml | 4 ++-- 5 files changed, 12 insertions(+), 13 deletions(-) diff --git a/trombinoscope/staff/TEMPLATE.yaml b/trombinoscope/staff/TEMPLATE.yaml index 5700618..f84b3e8 100644 --- a/trombinoscope/staff/TEMPLATE.yaml +++ b/trombinoscope/staff/TEMPLATE.yaml @@ -38,7 +38,7 @@ workplace: XXX University # affiliation: CNRS/INRAE/etc # -# The SouthGreen facility that you are part of. +# The SouthGreen facility that you are part of. # facility: iTrop # diff --git a/trombinoscope/staff/alexis-dereeper.yaml b/trombinoscope/staff/alexis-dereeper.yaml index 966d924..b2b1274 100644 --- a/trombinoscope/staff/alexis-dereeper.yaml +++ b/trombinoscope/staff/alexis-dereeper.yaml @@ -38,7 +38,7 @@ workplace: IRD Montpellier # affiliation: IRD # -# The SouthGreen facility that you are part of. +# The SouthGreen facility that you are part of. # facility: SouthGreen # @@ -47,7 +47,7 @@ facility: SouthGreen # proteomics, software, statistics, structure, systems biology, # dataservices, administration # -category: +category: - development - pathogen genomics - plant genomics @@ -78,7 +78,7 @@ keywords: - perl - python - rnaseq - - variants + - variants - SNP # # "role:" is the role that you play within your infrastructure. diff --git a/trombinoscope/staff/gaetan-droc.yaml b/trombinoscope/staff/gaetan-droc.yaml index bda340a..b9e9463 100644 --- a/trombinoscope/staff/gaetan-droc.yaml +++ b/trombinoscope/staff/gaetan-droc.yaml @@ -1,5 +1,4 @@ - ---- +--- staffname: Gaetan Droc type: staff @@ -19,7 +18,7 @@ affiliation: CIRAD facility: SouthGreen -category: +category: - development - software - annotation diff --git a/trombinoscope/staff/mathieu-rouard.yaml b/trombinoscope/staff/mathieu-rouard.yaml index 74e34b0..32b9491 100644 --- a/trombinoscope/staff/mathieu-rouard.yaml +++ b/trombinoscope/staff/mathieu-rouard.yaml @@ -14,10 +14,10 @@ city: workplace: Alliance Bioversity and CIAT affiliation: Bioversity International - UMR AGAP facility: SouthGreen -category: -- genomics -- software -- management +category: + - genomics + - software + - management bibtex: mathieu-rouard.bib orcid: 0000-0003-0284-1885 image: mathieu-rouard.jpg diff --git a/trombinoscope/staff/pierre-larmande.yaml b/trombinoscope/staff/pierre-larmande.yaml index 4a1fcf7..de88f84 100644 --- a/trombinoscope/staff/pierre-larmande.yaml +++ b/trombinoscope/staff/pierre-larmande.yaml @@ -11,7 +11,7 @@ # # Your real name, the exact way that you want it displayed. # -staffname: Pierre Larmande +staffname: Pierre Larmande # # Most people will have "type: staff", but some may be "affiliate". # @@ -38,7 +38,7 @@ workplace: IRD Montpellier # affiliation: IRD # -# The SouthGreen facility that you are part of. +# The SouthGreen facility that you are part of. # facility: SouthGreen # From 88dbf724bfc20880c1df2788ba4e1f61949e000e Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 20:36:40 +0100 Subject: [PATCH 15/19] fix yaml --- trombinoscope/staff/gaetan-droc.yaml | 17 ++++++++--------- trombinoscope/staff/pierre-larmande.yaml | 8 ++++---- trombinoscope/staff/valentin-guignon.yaml | 1 - 3 files changed, 12 insertions(+), 14 deletions(-) diff --git a/trombinoscope/staff/gaetan-droc.yaml b/trombinoscope/staff/gaetan-droc.yaml index b9e9463..22e7638 100644 --- a/trombinoscope/staff/gaetan-droc.yaml +++ b/trombinoscope/staff/gaetan-droc.yaml @@ -11,7 +11,7 @@ phone: xxx-xxx xx xx city: - Montpellier - + workplace: AGAP Unit affiliation: CIRAD @@ -24,7 +24,7 @@ category: - annotation - genomics - management - + bibtex: gaetan-droc.bib orcid: 0000-0003-1849-1269 @@ -38,14 +38,13 @@ keywords: - reproductible research - postgreql - web developpment - + role: Bioinformatician bio: Research engineer in Bioinformatics, part of SouthGreen sterring comittee. - My work involves NGS data analysis, including genome assembly, genome annotation, - comparative genomics, methylation analysis, and Cut&Tag, using Snakemake. - I actively participate in the development Genomes Hub through the integration of - omics data such as banana, rice, sugarcane, vanilla, coffea, cocoa. - - + My work involves NGS data analysis, including genome assembly, genome + annotation, comparative genomics, methylation analysis, and Cut&Tag, using + Snakemake. I actively participate in the development Genomes Hub through the + integration of omics data such as banana, rice, sugarcane, vanilla, coffea, + cocoa. diff --git a/trombinoscope/staff/pierre-larmande.yaml b/trombinoscope/staff/pierre-larmande.yaml index de88f84..d1553f0 100644 --- a/trombinoscope/staff/pierre-larmande.yaml +++ b/trombinoscope/staff/pierre-larmande.yaml @@ -47,7 +47,7 @@ facility: SouthGreen # proteomics, software, statistics, structure, systems biology, # dataservices, administration # -category: +category: - development - annotation - dataservices @@ -91,11 +91,11 @@ bio: Institute for Sustainable Development. He is member of the DIADE Unit in Montpellier. His main research interests are Data integration, Semantic Web, plant-ontologies, semantic data linking, Knowledge management and Big Data - for plant genomics. He obtained PhD in Informatics from the university of + for plant genomics. He obtained PhD in Informatics from the university of Montpellier in 2007 (about federated plant data integration approaches applied to agronomy) and recently obtained the habilitation to conduct - research supervision (HDR) in 2020. He coordinated the Oryza Tag Line + research supervision (HDR) in 2020. He coordinated the Oryza Tag Line phenotypic rice mutant database and was involved in the OrygenesDB T-DNA rice database. Pierre Larmande is the lead PI of the Agronomic Linked Data project (AgroLD), which is a Knowledge Graph database that consists of data - integrated from a variety of plant resources and ontologies. + integrated from a variety of plant resources and ontologies. diff --git a/trombinoscope/staff/valentin-guignon.yaml b/trombinoscope/staff/valentin-guignon.yaml index a11836a..ec06cef 100644 --- a/trombinoscope/staff/valentin-guignon.yaml +++ b/trombinoscope/staff/valentin-guignon.yaml @@ -46,4 +46,3 @@ bio: currently part of the Tripal Advisory Committee and the BrAPI Advisory Board. I have strong knowledge in databases and web development with an expertise on the Drupal CMS. I design algorithms, methodologies and software. - \ No newline at end of file From 8ad8c20714511a4b09e9d00a5e16faf46056f904 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 20:39:04 +0100 Subject: [PATCH 16/19] fix yaml --- trombinoscope/staff/gaetan-droc.yaml | 2 +- trombinoscope/staff/mathieu-rouard.yaml | 64 ++++++++++++------------- 2 files changed, 33 insertions(+), 33 deletions(-) diff --git a/trombinoscope/staff/gaetan-droc.yaml b/trombinoscope/staff/gaetan-droc.yaml index 22e7638..f703e0a 100644 --- a/trombinoscope/staff/gaetan-droc.yaml +++ b/trombinoscope/staff/gaetan-droc.yaml @@ -43,7 +43,7 @@ role: Bioinformatician bio: Research engineer in Bioinformatics, part of SouthGreen sterring comittee. - My work involves NGS data analysis, including genome assembly, genome + My work involves NGS data analysis, including genome assembly, genome annotation, comparative genomics, methylation analysis, and Cut&Tag, using Snakemake. I actively participate in the development Genomes Hub through the integration of omics data such as banana, rice, sugarcane, vanilla, coffea, diff --git a/trombinoscope/staff/mathieu-rouard.yaml b/trombinoscope/staff/mathieu-rouard.yaml index 32b9491..b6569c3 100644 --- a/trombinoscope/staff/mathieu-rouard.yaml +++ b/trombinoscope/staff/mathieu-rouard.yaml @@ -1,32 +1,32 @@ ---- -staffname: Mathieu Rouard -type: staff -bio: - Research scientist in Bioinformatics, part of SG sterring comittee - I am involved in genome analyses and contribute to related - web resources development. Strong focus on banana and genetic diversity. - -active: true -email: m.rouard@cgiar.org -phone: xxx-xxx xx xx -city: - - Montpellier -workplace: Alliance Bioversity and CIAT -affiliation: Bioversity International - UMR AGAP -facility: SouthGreen -category: - - genomics - - software - - management -bibtex: mathieu-rouard.bib -orcid: 0000-0003-0284-1885 -image: mathieu-rouard.jpg -keywords: - - Genome Hubs - - Banana Genomes - - Orthology - - Gene families - - rnaseq - - Gigwa - - Interoperability -role: Comité de pilotage +--- +staffname: Mathieu Rouard +type: staff +bio: + Research scientist in Bioinformatics, part of SG sterring comittee + I am involved in genome analyses and contribute to related + web resources development. Strong focus on banana and genetic diversity. + +active: true +email: m.rouard@cgiar.org +phone: xxx-xxx xx xx +city: + - Montpellier +workplace: Alliance Bioversity and CIAT +affiliation: Bioversity International - UMR AGAP +facility: SouthGreen +category: + - genomics + - software + - management +bibtex: mathieu-rouard.bib +orcid: 0000-0003-0284-1885 +image: mathieu-rouard.jpg +keywords: + - Genome Hubs + - Banana Genomes + - Orthology + - Gene families + - rnaseq + - Gigwa + - Interoperability +role: Comité de pilotage From 4735dccadd83901779493e9b8fd9aba1e130d231 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 20:41:32 +0100 Subject: [PATCH 17/19] Update build.yaml --- .github/workflows/build.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index c0d2523..30fa22b 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -17,7 +17,7 @@ concurrency: jobs: build: - if: ${{ github.event.workflow_run.conclusion == 'success' }} +# if: ${{ github.event.workflow_run.conclusion == 'success' }} runs-on: ubuntu-22.04 steps: From 4d314d80d7061018082f0542f7714a171d0d511d Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 20:44:05 +0100 Subject: [PATCH 18/19] Update build.yaml --- .github/workflows/build.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 30fa22b..458961d 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -17,9 +17,10 @@ concurrency: jobs: build: -# if: ${{ github.event.workflow_run.conclusion == 'success' }} - runs-on: ubuntu-22.04 + runs-on: ubuntu-22.04 + if: ${{ github.event.workflow_run.conclusion == 'success' }} + steps: - uses: actions/checkout@v3 - uses: r-lib/actions/setup-r@v2 From eafd4b9c8024c84f855bfe76f4d7adb97c05c7fd Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 26 Mar 2024 21:26:36 +0100 Subject: [PATCH 19/19] Update build.yaml --- .github/workflows/build.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 458961d..5341d07 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -19,7 +19,7 @@ jobs: build: runs-on: ubuntu-22.04 - if: ${{ github.event.workflow_run.conclusion == 'success' }} + #if: ${{ github.event.workflow_run.conclusion == 'success' }} steps: - uses: actions/checkout@v3