From 7be8c88de69e57b009fdca70c238e3bb78ec4a7c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 10 Feb 2022 15:37:34 +0100 Subject: [PATCH 1/9] Update citations-eu-manual.bib --- _bibliography/citations-eu-manual.bib | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/_bibliography/citations-eu-manual.bib b/_bibliography/citations-eu-manual.bib index 47d6f645c..26c084489 100644 --- a/_bibliography/citations-eu-manual.bib +++ b/_bibliography/citations-eu-manual.bib @@ -7,6 +7,19 @@ @article{arcari2022interplay publisher={Springer} } +@article{Gao2022, + doi = {10.1038/s41467-022-28434-1}, + url = {https://doi.org/10.1038/s41467-022-28434-1}, + year = {2022}, + month = feb, + publisher = {Springer Science and Business Media {LLC}}, + volume = {13}, + number = {1}, + author = {Meijiang Gao and Marina Veil and Marcus Rosenblatt and Aileen Julia Riesle and Anna Gebhard and Helge Hass and Lenka Buryanova and Lev Y. Yampolsky and Bj\"{o}rn Gr\"{u}ning and Sergey V. Ulianov and Jens Timmer and Daria Onichtchouk}, + title = {Pluripotency factors determine gene expression repertoire at zygotic genome activation}, + journal = {Nature Communications} +} + @article{lucaci2022rascl, title={RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis}, author={Lucaci, Alexander G and Zehr, Jordan D and Shank, Stephen D and Bouvier, Dave and Mei, Han and Nekrutenko, Anton and Martin, Darren P and Pond, Sergei}, From ba8b220ed5bf9e91ff8c8bebabbc59880e652957 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 10 Feb 2022 15:38:00 +0100 Subject: [PATCH 2/9] Update freiburg.bib --- _bibliography/freiburg.bib | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/_bibliography/freiburg.bib b/_bibliography/freiburg.bib index 65e5e583a..8e0eb5c3c 100644 --- a/_bibliography/freiburg.bib +++ b/_bibliography/freiburg.bib @@ -4,6 +4,19 @@ # Publications +@article{Gao2022, + doi = {10.1038/s41467-022-28434-1}, + url = {https://doi.org/10.1038/s41467-022-28434-1}, + year = {2022}, + month = feb, + publisher = {Springer Science and Business Media {LLC}}, + volume = {13}, + number = {1}, + author = {Meijiang Gao and Marina Veil and Marcus Rosenblatt and Aileen Julia Riesle and Anna Gebhard and Helge Hass and Lenka Buryanova and Lev Y. Yampolsky and Bj\"{o}rn Gr\"{u}ning and Sergey V. Ulianov and Jens Timmer and Daria Onichtchouk}, + title = {Pluripotency factors determine gene expression repertoire at zygotic genome activation}, + journal = {Nature Communications} +} + @article{Dai2021, doi = {10.1038/s41467-021-26111-3}, url = {https://doi.org/10.1038/s41467-021-26111-3}, From d42ae6e0e1a7e58ea90a794d15f77406d0f3f6c3 Mon Sep 17 00:00:00 2001 From: "UseGalaxy.EU Jenkins Bot" Date: Thu, 10 Feb 2022 17:39:10 +0100 Subject: [PATCH 3/9] Autoupdate tool blog post --- _posts/2022-02-10-tool-update.md | 95 ++++++++++++++++++++++++++++++++ 1 file changed, 95 insertions(+) create mode 100644 _posts/2022-02-10-tool-update.md diff --git a/_posts/2022-02-10-tool-update.md b/_posts/2022-02-10-tool-update.md new file mode 100644 index 000000000..e3bd8cfbe --- /dev/null +++ b/_posts/2022-02-10-tool-update.md @@ -0,0 +1,95 @@ +--- +site: freiburg +tags: [tools] +title: UseGalaxy.eu Tool Updates for 2022-02-10 +supporters: +- denbi +- elixir +--- + +On 2022-02-10, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in [Jenkins Build #311](https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#311/) + + +## Variant Calling + +- bcftools_annotate was updated to [403553ae19f6](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_annotate/403553ae19f6) +- bcftools_call was updated to [072f606e2e69](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_call/072f606e2e69) +- bcftools_call was updated to [5801eff9ac7e](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_call/5801eff9ac7e) +- bcftools_concat was updated to [874cc12ae316](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_concat/874cc12ae316) +- bcftools_concat was updated to [d40d4bf05718](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_concat/d40d4bf05718) +- bcftools_consensus was updated to [d6dc477167f8](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_consensus/d6dc477167f8) +- bcftools_convert_from_vcf was updated to [b8e9da766b0f](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_from_vcf/b8e9da766b0f) +- bcftools_convert_to_vcf was updated to [fec517907949](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_to_vcf/fec517907949) +- bcftools_csq was updated to [f10f5b4e7854](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_csq/f10f5b4e7854) +- bcftools_csq was updated to [fdd127bd4a32](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_csq/fdd127bd4a32) +- bcftools_filter was updated to [6ca7c55a27e8](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_filter/6ca7c55a27e8) +- bcftools_gtcheck was updated to [672b6c02fbc7](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_gtcheck/672b6c02fbc7) +- bcftools_isec was updated to [02f349bdbf96](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_isec/02f349bdbf96) +- bcftools_merge was updated to [9473302f4588](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_merge/9473302f4588) +- bcftools_merge was updated to [e03f2f3ac3a9](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_merge/e03f2f3ac3a9) +- bcftools_mpileup was updated to [0dbff46d5a1b](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_mpileup/0dbff46d5a1b) +- bcftools_norm was updated to [a62e934346f5](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_norm/a62e934346f5) +- bcftools_norm was updated to [c077f71d351f](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_norm/c077f71d351f) +- bcftools_plugin_color_chrs was updated to [71dfde92fd57](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_color_chrs/71dfde92fd57) +- bcftools_plugin_color_chrs was updated to [c39113e2ae34](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_color_chrs/c39113e2ae34) +- bcftools_plugin_frameshifts was updated to [48ac4d611e92](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_frameshifts/48ac4d611e92) +- bcftools_plugin_frameshifts was updated to [eb22990a2be9](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_frameshifts/eb22990a2be9) +- bcftools_query was updated to [c9c5718edc19](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_query/c9c5718edc19) +- bcftools_reheader was updated to [9ef52d95114b](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_reheader/9ef52d95114b) +- bcftools_roh was updated to [b76adb2f1c51](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_roh/b76adb2f1c51) +- bcftools_view was updated to [98d5499ead46](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_view/98d5499ead46) + +## FASTA/FASTQ + +- cutadapt was updated to [48f587c13075](https://toolshed.g2.bx.psu.edu/view/lparsons/cutadapt/48f587c13075) + +## Assembly + +- quast was updated to [875d0f36d66f](https://toolshed.g2.bx.psu.edu/view/iuc/quast/875d0f36d66f) +- rnaspades was updated to [53c2bc8c2ae3](https://toolshed.g2.bx.psu.edu/view/iuc/rnaspades/53c2bc8c2ae3) +- spades_biosyntheticspades was updated to [7490b213baa9](https://toolshed.g2.bx.psu.edu/view/iuc/spades_biosyntheticspades/7490b213baa9) +- spades_coronaspades was updated to [d6e617c4e338](https://toolshed.g2.bx.psu.edu/view/iuc/spades_coronaspades/d6e617c4e338) +- spades_metaplasmidspades was updated to [b8002c3f7141](https://toolshed.g2.bx.psu.edu/view/iuc/spades_metaplasmidspades/b8002c3f7141) +- spades_metaviralspades was updated to [2a10645aeadd](https://toolshed.g2.bx.psu.edu/view/iuc/spades_metaviralspades/2a10645aeadd) +- spades_plasmidspades was updated to [340bc17f49cf](https://toolshed.g2.bx.psu.edu/view/iuc/spades_plasmidspades/340bc17f49cf) +- spades_rnaviralspades was updated to [d159735a6a9f](https://toolshed.g2.bx.psu.edu/view/iuc/spades_rnaviralspades/d159735a6a9f) +- metaspades was updated to [e731ea24e48d](https://toolshed.g2.bx.psu.edu/view/nml/metaspades/e731ea24e48d) +- spades was updated to [7897763d14ec](https://toolshed.g2.bx.psu.edu/view/nml/spades/7897763d14ec) + +## RNA Analysis + +- trinity_gene_to_trans_map was updated to [964b7efe2639](https://toolshed.g2.bx.psu.edu/view/iuc/trinity_gene_to_trans_map/964b7efe2639) + +## Metagenomic Analysis + +- data_manager_build_bracken_database was updated to [fd5830f88314](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_bracken_database/fd5830f88314) + +## ChemicalToolBox + +- gmx_get_builtin_file was updated to [a81256d23782](https://toolshed.g2.bx.psu.edu/view/chemteam/gmx_get_builtin_file/a81256d23782) +- gromacs_extract_topology was updated to [9faa4f4b8b76](https://toolshed.g2.bx.psu.edu/view/chemteam/gromacs_extract_topology/9faa4f4b8b76) +- gromacs_modify_topology was updated to [5521a057ed6a](https://toolshed.g2.bx.psu.edu/view/chemteam/gromacs_modify_topology/5521a057ed6a) + +## Proteomics + +- openms_openpepxl was updated to [40cc19c0dbd6](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/40cc19c0dbd6) +- openms_openpepxl was updated to [a2a842b00f9c](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/a2a842b00f9c) +- openms_openpepxl was updated to [fc36cfd19834](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/fc36cfd19834) +- openms_percolatoradapter was updated to [0fc9ae55bcfc](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/0fc9ae55bcfc) +- openms_percolatoradapter was updated to [e7881a82b56d](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/e7881a82b56d) +- openms_xfdr was updated to [81402a5e4173](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/81402a5e4173) +- openms_xfdr was updated to [9a6e3bb0f358](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/9a6e3bb0f358) + +## Single-cell + +- music_compare was updated to [10bf0f89035f](https://toolshed.g2.bx.psu.edu/view/bgruening/music_compare/10bf0f89035f) +- music_construct_eset was updated to [7ffaa0968da3](https://toolshed.g2.bx.psu.edu/view/bgruening/music_construct_eset/7ffaa0968da3) +- music_deconvolution was updated to [56371b5a2da9](https://toolshed.g2.bx.psu.edu/view/bgruening/music_deconvolution/56371b5a2da9) +- music_inspect_eset was updated to [8c64a2da3869](https://toolshed.g2.bx.psu.edu/view/bgruening/music_inspect_eset/8c64a2da3869) + +## Annotation + +- maker was updated to [a444254e9a57](https://toolshed.g2.bx.psu.edu/view/iuc/maker/a444254e9a57) +- maker_map_ids was updated to [9e0cc465595e](https://toolshed.g2.bx.psu.edu/view/iuc/maker_map_ids/9e0cc465595e) +- maker_map_ids was updated to [e906fa778440](https://toolshed.g2.bx.psu.edu/view/iuc/maker_map_ids/e906fa778440) + From 5ed40fd4666ece066ec92b87d9984d3ad9d6bd62 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 10 Feb 2022 21:15:12 +0100 Subject: [PATCH 4/9] Delete 2022-02-10-tool-update.md --- _posts/2022-02-10-tool-update.md | 95 -------------------------------- 1 file changed, 95 deletions(-) delete mode 100644 _posts/2022-02-10-tool-update.md diff --git a/_posts/2022-02-10-tool-update.md b/_posts/2022-02-10-tool-update.md deleted file mode 100644 index e3bd8cfbe..000000000 --- a/_posts/2022-02-10-tool-update.md +++ /dev/null @@ -1,95 +0,0 @@ ---- -site: freiburg -tags: [tools] -title: UseGalaxy.eu Tool Updates for 2022-02-10 -supporters: -- denbi -- elixir ---- - -On 2022-02-10, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in [Jenkins Build #311](https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#311/) - - -## Variant Calling - -- bcftools_annotate was updated to [403553ae19f6](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_annotate/403553ae19f6) -- bcftools_call was updated to [072f606e2e69](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_call/072f606e2e69) -- bcftools_call was updated to [5801eff9ac7e](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_call/5801eff9ac7e) -- bcftools_concat was updated to [874cc12ae316](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_concat/874cc12ae316) -- bcftools_concat was updated to [d40d4bf05718](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_concat/d40d4bf05718) -- bcftools_consensus was updated to [d6dc477167f8](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_consensus/d6dc477167f8) -- bcftools_convert_from_vcf was updated to [b8e9da766b0f](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_from_vcf/b8e9da766b0f) -- bcftools_convert_to_vcf was updated to [fec517907949](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_to_vcf/fec517907949) -- bcftools_csq was updated to [f10f5b4e7854](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_csq/f10f5b4e7854) -- bcftools_csq was updated to [fdd127bd4a32](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_csq/fdd127bd4a32) -- bcftools_filter was updated to [6ca7c55a27e8](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_filter/6ca7c55a27e8) -- bcftools_gtcheck was updated to [672b6c02fbc7](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_gtcheck/672b6c02fbc7) -- bcftools_isec was updated to [02f349bdbf96](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_isec/02f349bdbf96) -- bcftools_merge was updated to [9473302f4588](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_merge/9473302f4588) -- bcftools_merge was updated to [e03f2f3ac3a9](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_merge/e03f2f3ac3a9) -- bcftools_mpileup was updated to [0dbff46d5a1b](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_mpileup/0dbff46d5a1b) -- bcftools_norm was updated to [a62e934346f5](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_norm/a62e934346f5) -- bcftools_norm was updated to [c077f71d351f](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_norm/c077f71d351f) -- bcftools_plugin_color_chrs was updated to [71dfde92fd57](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_color_chrs/71dfde92fd57) -- bcftools_plugin_color_chrs was updated to [c39113e2ae34](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_color_chrs/c39113e2ae34) -- bcftools_plugin_frameshifts was updated to [48ac4d611e92](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_frameshifts/48ac4d611e92) -- bcftools_plugin_frameshifts was updated to [eb22990a2be9](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_frameshifts/eb22990a2be9) -- bcftools_query was updated to [c9c5718edc19](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_query/c9c5718edc19) -- bcftools_reheader was updated to [9ef52d95114b](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_reheader/9ef52d95114b) -- bcftools_roh was updated to [b76adb2f1c51](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_roh/b76adb2f1c51) -- bcftools_view was updated to [98d5499ead46](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_view/98d5499ead46) - -## FASTA/FASTQ - -- cutadapt was updated to [48f587c13075](https://toolshed.g2.bx.psu.edu/view/lparsons/cutadapt/48f587c13075) - -## Assembly - -- quast was updated to [875d0f36d66f](https://toolshed.g2.bx.psu.edu/view/iuc/quast/875d0f36d66f) -- rnaspades was updated to [53c2bc8c2ae3](https://toolshed.g2.bx.psu.edu/view/iuc/rnaspades/53c2bc8c2ae3) -- spades_biosyntheticspades was updated to [7490b213baa9](https://toolshed.g2.bx.psu.edu/view/iuc/spades_biosyntheticspades/7490b213baa9) -- spades_coronaspades was updated to [d6e617c4e338](https://toolshed.g2.bx.psu.edu/view/iuc/spades_coronaspades/d6e617c4e338) -- spades_metaplasmidspades was updated to [b8002c3f7141](https://toolshed.g2.bx.psu.edu/view/iuc/spades_metaplasmidspades/b8002c3f7141) -- spades_metaviralspades was updated to [2a10645aeadd](https://toolshed.g2.bx.psu.edu/view/iuc/spades_metaviralspades/2a10645aeadd) -- spades_plasmidspades was updated to [340bc17f49cf](https://toolshed.g2.bx.psu.edu/view/iuc/spades_plasmidspades/340bc17f49cf) -- spades_rnaviralspades was updated to [d159735a6a9f](https://toolshed.g2.bx.psu.edu/view/iuc/spades_rnaviralspades/d159735a6a9f) -- metaspades was updated to [e731ea24e48d](https://toolshed.g2.bx.psu.edu/view/nml/metaspades/e731ea24e48d) -- spades was updated to [7897763d14ec](https://toolshed.g2.bx.psu.edu/view/nml/spades/7897763d14ec) - -## RNA Analysis - -- trinity_gene_to_trans_map was updated to [964b7efe2639](https://toolshed.g2.bx.psu.edu/view/iuc/trinity_gene_to_trans_map/964b7efe2639) - -## Metagenomic Analysis - -- data_manager_build_bracken_database was updated to [fd5830f88314](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_bracken_database/fd5830f88314) - -## ChemicalToolBox - -- gmx_get_builtin_file was updated to [a81256d23782](https://toolshed.g2.bx.psu.edu/view/chemteam/gmx_get_builtin_file/a81256d23782) -- gromacs_extract_topology was updated to [9faa4f4b8b76](https://toolshed.g2.bx.psu.edu/view/chemteam/gromacs_extract_topology/9faa4f4b8b76) -- gromacs_modify_topology was updated to [5521a057ed6a](https://toolshed.g2.bx.psu.edu/view/chemteam/gromacs_modify_topology/5521a057ed6a) - -## Proteomics - -- openms_openpepxl was updated to [40cc19c0dbd6](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/40cc19c0dbd6) -- openms_openpepxl was updated to [a2a842b00f9c](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/a2a842b00f9c) -- openms_openpepxl was updated to [fc36cfd19834](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/fc36cfd19834) -- openms_percolatoradapter was updated to [0fc9ae55bcfc](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/0fc9ae55bcfc) -- openms_percolatoradapter was updated to [e7881a82b56d](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/e7881a82b56d) -- openms_xfdr was updated to [81402a5e4173](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/81402a5e4173) -- openms_xfdr was updated to [9a6e3bb0f358](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/9a6e3bb0f358) - -## Single-cell - -- music_compare was updated to [10bf0f89035f](https://toolshed.g2.bx.psu.edu/view/bgruening/music_compare/10bf0f89035f) -- music_construct_eset was updated to [7ffaa0968da3](https://toolshed.g2.bx.psu.edu/view/bgruening/music_construct_eset/7ffaa0968da3) -- music_deconvolution was updated to [56371b5a2da9](https://toolshed.g2.bx.psu.edu/view/bgruening/music_deconvolution/56371b5a2da9) -- music_inspect_eset was updated to [8c64a2da3869](https://toolshed.g2.bx.psu.edu/view/bgruening/music_inspect_eset/8c64a2da3869) - -## Annotation - -- maker was updated to [a444254e9a57](https://toolshed.g2.bx.psu.edu/view/iuc/maker/a444254e9a57) -- maker_map_ids was updated to [9e0cc465595e](https://toolshed.g2.bx.psu.edu/view/iuc/maker_map_ids/9e0cc465595e) -- maker_map_ids was updated to [e906fa778440](https://toolshed.g2.bx.psu.edu/view/iuc/maker_map_ids/e906fa778440) - From 0af1371bcbaa265ded0b28072e0a35dd3000eaf1 Mon Sep 17 00:00:00 2001 From: "UseGalaxy.EU Jenkins Bot" Date: Sun, 13 Feb 2022 12:29:33 +0100 Subject: [PATCH 5/9] Autoupdate tool blog post --- _posts/2022-02-13-tool-update.md | 78 ++++++++++++++++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 _posts/2022-02-13-tool-update.md diff --git a/_posts/2022-02-13-tool-update.md b/_posts/2022-02-13-tool-update.md new file mode 100644 index 000000000..4b68c1b25 --- /dev/null +++ b/_posts/2022-02-13-tool-update.md @@ -0,0 +1,78 @@ +--- +site: freiburg +tags: [tools] +title: UseGalaxy.eu Tool Updates for 2022-02-13 +supporters: +- denbi +- elixir +--- + +On 2022-02-13, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in [Jenkins Build #312](https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#312/) + + +## Variant Calling + +- bcftools_annotate was updated to [403553ae19f6](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_annotate/403553ae19f6) +- bcftools_call was updated to [072f606e2e69](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_call/072f606e2e69) +- bcftools_call was updated to [5801eff9ac7e](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_call/5801eff9ac7e) +- bcftools_concat was updated to [874cc12ae316](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_concat/874cc12ae316) +- bcftools_concat was updated to [d40d4bf05718](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_concat/d40d4bf05718) +- bcftools_consensus was updated to [d6dc477167f8](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_consensus/d6dc477167f8) +- bcftools_convert_from_vcf was updated to [b8e9da766b0f](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_from_vcf/b8e9da766b0f) +- bcftools_convert_to_vcf was updated to [fec517907949](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_to_vcf/fec517907949) +- bcftools_csq was updated to [f10f5b4e7854](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_csq/f10f5b4e7854) +- bcftools_csq was updated to [fdd127bd4a32](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_csq/fdd127bd4a32) +- bcftools_filter was updated to [6ca7c55a27e8](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_filter/6ca7c55a27e8) +- bcftools_gtcheck was updated to [672b6c02fbc7](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_gtcheck/672b6c02fbc7) +- bcftools_isec was updated to [02f349bdbf96](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_isec/02f349bdbf96) +- bcftools_merge was updated to [9473302f4588](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_merge/9473302f4588) +- bcftools_merge was updated to [e03f2f3ac3a9](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_merge/e03f2f3ac3a9) +- bcftools_mpileup was updated to [0dbff46d5a1b](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_mpileup/0dbff46d5a1b) +- bcftools_norm was updated to [a62e934346f5](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_norm/a62e934346f5) +- bcftools_norm was updated to [c077f71d351f](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_norm/c077f71d351f) +- bcftools_plugin_color_chrs was updated to [71dfde92fd57](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_color_chrs/71dfde92fd57) +- bcftools_plugin_color_chrs was updated to [c39113e2ae34](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_color_chrs/c39113e2ae34) +- bcftools_plugin_frameshifts was updated to [48ac4d611e92](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_frameshifts/48ac4d611e92) +- bcftools_plugin_frameshifts was updated to [eb22990a2be9](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_frameshifts/eb22990a2be9) +- bcftools_query was updated to [c9c5718edc19](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_query/c9c5718edc19) +- bcftools_reheader was updated to [9ef52d95114b](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_reheader/9ef52d95114b) +- bcftools_roh was updated to [b76adb2f1c51](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_roh/b76adb2f1c51) +- bcftools_view was updated to [98d5499ead46](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_view/98d5499ead46) + +## Proteomics + +- openms_openpepxl was updated to [a2a842b00f9c](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/a2a842b00f9c) +- openms_percolatoradapter was updated to [0fc9ae55bcfc](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/0fc9ae55bcfc) +- openms_percolatoradapter was updated to [e7881a82b56d](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/e7881a82b56d) +- openms_xfdr was updated to [81402a5e4173](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/81402a5e4173) +- openms_xfdr was updated to [9a6e3bb0f358](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/9a6e3bb0f358) + +## Metagenomic Analysis + +- lotus2 was updated to [6e9fd3e0dcbb](https://toolshed.g2.bx.psu.edu/view/earlhaminst/lotus2/6e9fd3e0dcbb) + +## Annotation + +- interproscan was updated to [c55643c3d813](https://toolshed.g2.bx.psu.edu/view/bgruening/interproscan/c55643c3d813) + +## deepTools + +- deeptools_alignmentsieve was updated to [e5a296ce8fbb](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_alignmentsieve/e5a296ce8fbb) +- deeptools_bam_compare was updated to [c89b665b45e4](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_compare/c89b665b45e4) +- deeptools_bam_coverage was updated to [4df95152a39e](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_coverage/4df95152a39e) +- deeptools_bam_pe_fragmentsize was updated to [3f9dc453c0e8](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_pe_fragmentsize/3f9dc453c0e8) +- deeptools_bigwig_compare was updated to [7989c6ddf634](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bigwig_compare/7989c6ddf634) +- deeptools_compute_gc_bias was updated to [56d5b797ce84](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_compute_gc_bias/56d5b797ce84) +- deeptools_compute_matrix was updated to [19bb3e6d9e31](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_compute_matrix/19bb3e6d9e31) +- deeptools_compute_matrix_operations was updated to [be95d48dd27f](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_compute_matrix_operations/be95d48dd27f) +- deeptools_correct_gc_bias was updated to [00a71ff7c06b](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_correct_gc_bias/00a71ff7c06b) +- deeptools_multi_bam_summary was updated to [b4e53394fced](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_multi_bam_summary/b4e53394fced) +- deeptools_multi_bigwig_summary was updated to [459cfa861f0b](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_multi_bigwig_summary/459cfa861f0b) +- deeptools_plot_correlation was updated to [e44978659400](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_correlation/e44978659400) +- deeptools_plot_coverage was updated to [7fda5607e777](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_coverage/7fda5607e777) +- deeptools_plot_enrichment was updated to [88ce7fed1488](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_enrichment/88ce7fed1488) +- deeptools_plot_fingerprint was updated to [ca8a7f0ea872](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_fingerprint/ca8a7f0ea872) +- deeptools_plot_heatmap was updated to [42cb23d80271](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_heatmap/42cb23d80271) +- deeptools_plot_pca was updated to [7784523d9743](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_pca/7784523d9743) +- deeptools_plot_profile was updated to [e9429e484e25](https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_profile/e9429e484e25) + From ff9068aed972b56101eeebb3bd3f0a2f7cc4ecd5 Mon Sep 17 00:00:00 2001 From: OlegZharkov Date: Sun, 13 Feb 2022 23:01:01 +0000 Subject: [PATCH 6/9] Update tools --- tools.md | 56 ++++++++++++++++++++++++++++++-------------------------- 1 file changed, 30 insertions(+), 26 deletions(-) diff --git a/tools.md b/tools.md index 35ae8d080..5898606c2 100644 --- a/tools.md +++ b/tools.md @@ -2,7 +2,7 @@ layout: default --- -# European Galaxy tools (2815 and counting) +# European Galaxy tools (2819 and counting)

Get Data

@@ -245,8 +245,8 @@ layout: default

FASTA/FASTQ

- + @@ -559,6 +559,7 @@ layout: default

Genomics Analysis

Annotation

+ @@ -588,7 +589,6 @@ layout: default - @@ -725,10 +725,17 @@ layout: default

Assembly

- + + + + + + + + @@ -737,7 +744,6 @@ layout: default - @@ -757,11 +763,6 @@ layout: default - - - - - @@ -771,7 +772,6 @@ layout: default - @@ -963,6 +963,7 @@ layout: default

RNA-Seq

RNA Analysis

+ @@ -1057,7 +1058,6 @@ layout: default - @@ -1256,12 +1256,13 @@ layout: default

Single-cell

+ + - @@ -1328,23 +1329,23 @@ layout: default

deepTools

- + + + + - - - - - - - - - - - + + + + + + + +

Gemini

@@ -1618,6 +1619,7 @@ layout: default

Metagenomics

Metagenomic Analysis

+ @@ -1650,7 +1652,6 @@ layout: default - @@ -2267,6 +2268,8 @@ layout: default

ChemicalToolBox

+ + @@ -2310,6 +2313,7 @@ layout: default + From ee8d7c4d6ce0aa9270f9f98abf893fc62dffa786 Mon Sep 17 00:00:00 2001 From: "UseGalaxy.EU Jenkins Bot" Date: Mon, 14 Feb 2022 17:13:48 +0100 Subject: [PATCH 7/9] Autoupdate tool blog post --- _posts/2022-02-14-tool-update.md | 69 ++++++++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 _posts/2022-02-14-tool-update.md diff --git a/_posts/2022-02-14-tool-update.md b/_posts/2022-02-14-tool-update.md new file mode 100644 index 000000000..bdf0ac764 --- /dev/null +++ b/_posts/2022-02-14-tool-update.md @@ -0,0 +1,69 @@ +--- +site: freiburg +tags: [tools] +title: UseGalaxy.eu Tool Updates for 2022-02-14 +supporters: +- denbi +- elixir +--- + +On 2022-02-14, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in [Jenkins Build #313](https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#313/) + + +## Variant Calling + +- bcftools_annotate was updated to [403553ae19f6](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_annotate/403553ae19f6) +- bcftools_call was updated to [072f606e2e69](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_call/072f606e2e69) +- bcftools_call was updated to [5801eff9ac7e](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_call/5801eff9ac7e) +- bcftools_concat was updated to [874cc12ae316](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_concat/874cc12ae316) +- bcftools_concat was updated to [d40d4bf05718](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_concat/d40d4bf05718) +- bcftools_consensus was updated to [d6dc477167f8](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_consensus/d6dc477167f8) +- bcftools_convert_from_vcf was updated to [b8e9da766b0f](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_from_vcf/b8e9da766b0f) +- bcftools_convert_to_vcf was updated to [fec517907949](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_to_vcf/fec517907949) +- bcftools_csq was updated to [f10f5b4e7854](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_csq/f10f5b4e7854) +- bcftools_csq was updated to [fdd127bd4a32](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_csq/fdd127bd4a32) +- bcftools_filter was updated to [6ca7c55a27e8](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_filter/6ca7c55a27e8) +- bcftools_gtcheck was updated to [672b6c02fbc7](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_gtcheck/672b6c02fbc7) +- bcftools_isec was updated to [02f349bdbf96](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_isec/02f349bdbf96) +- bcftools_merge was updated to [9473302f4588](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_merge/9473302f4588) +- bcftools_merge was updated to [e03f2f3ac3a9](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_merge/e03f2f3ac3a9) +- bcftools_mpileup was updated to [0dbff46d5a1b](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_mpileup/0dbff46d5a1b) +- bcftools_norm was updated to [a62e934346f5](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_norm/a62e934346f5) +- bcftools_norm was updated to [c077f71d351f](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_norm/c077f71d351f) +- bcftools_plugin_color_chrs was updated to [71dfde92fd57](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_color_chrs/71dfde92fd57) +- bcftools_plugin_color_chrs was updated to [c39113e2ae34](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_color_chrs/c39113e2ae34) +- bcftools_plugin_frameshifts was updated to [48ac4d611e92](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_frameshifts/48ac4d611e92) +- bcftools_plugin_frameshifts was updated to [eb22990a2be9](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_frameshifts/eb22990a2be9) +- bcftools_query was updated to [c9c5718edc19](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_query/c9c5718edc19) +- bcftools_reheader was updated to [9ef52d95114b](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_reheader/9ef52d95114b) +- bcftools_roh was updated to [b76adb2f1c51](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_roh/b76adb2f1c51) +- bcftools_view was updated to [98d5499ead46](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_view/98d5499ead46) + +## Metagenomic Analysis + +- drep_compare was updated to [7157accd23d0](https://toolshed.g2.bx.psu.edu/view/iuc/drep_compare/7157accd23d0) +- drep_dereplicate was updated to [ef7cd2e7bc05](https://toolshed.g2.bx.psu.edu/view/iuc/drep_dereplicate/ef7cd2e7bc05) + +## Graph/Display Data + +- pygenometracks was updated to [a1abfa420d9d](https://toolshed.g2.bx.psu.edu/view/iuc/pygenometracks/a1abfa420d9d) + +## Assembly + +- hifiasm was updated to [5bec28269d95](https://toolshed.g2.bx.psu.edu/view/bgruening/hifiasm/5bec28269d95) + +## Phylogenetics + +- pangolin was updated to [2fa9d4f1b48f](https://toolshed.g2.bx.psu.edu/view/iuc/pangolin/2fa9d4f1b48f) + +## Proteomics + +- eggnog_mapper was updated to [63662ae295d6](https://toolshed.g2.bx.psu.edu/view/galaxyp/eggnog_mapper/63662ae295d6) +- openms_openpepxl was updated to [40cc19c0dbd6](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/40cc19c0dbd6) +- openms_openpepxl was updated to [a2a842b00f9c](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/a2a842b00f9c) +- openms_openpepxl was updated to [fc36cfd19834](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/fc36cfd19834) +- openms_percolatoradapter was updated to [0fc9ae55bcfc](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/0fc9ae55bcfc) +- openms_percolatoradapter was updated to [e7881a82b56d](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/e7881a82b56d) +- openms_xfdr was updated to [81402a5e4173](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/81402a5e4173) +- openms_xfdr was updated to [9a6e3bb0f358](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/9a6e3bb0f358) + From 0ee35bfc2bf89f1c071ec2f78f838a4d2a31bb31 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Mon, 14 Feb 2022 19:27:01 +0100 Subject: [PATCH 8/9] Update Freiburg Feb 2002 workshop with some links --- _events/2021-12-23-GalaxyWS_SFB.md | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/_events/2021-12-23-GalaxyWS_SFB.md b/_events/2021-12-23-GalaxyWS_SFB.md index 6c5826180..28e994b8a 100644 --- a/_events/2021-12-23-GalaxyWS_SFB.md +++ b/_events/2021-12-23-GalaxyWS_SFB.md @@ -23,7 +23,7 @@ online course and is limited to the members CRC 1425, CRC 992 and MeInBio. ## Venue -Online +[Online](https://usegalaxy.eu/join-training/fr-feb-2022) ## Program @@ -43,6 +43,11 @@ Fri | Advanced Galaxy features, discussions, bring your own data. ## Links +* Zoom meeting room for Galaxy traning and Q&A sessions: [https://uni-freiburg.zoom.us/j/62060189065?pwd=Vmg4MElrWkl4M2xyLy9lSGY2bm9nUT09](https://uni-freiburg.zoom.us/j/62060189065?pwd=Vmg4MElrWkl4M2xyLy9lSGY2bm9nUT09) + - Topic: Galaxy Workshop February 2022 + - Meeting ID: 620 6018 9065 + - Passcode: aPE9j8WXi +* Slack channel for discussions during the hands-on: [link](https://app.slack.com/accept-shared-channel/T032SC3N5GE/I0319JJBQHZ/enQtMzA0MzYzMDM5ODYxMS05NTViYTcyODUxZGUxZmY0N2QwMGY2NGE3YzA4YmMwOTMwNGNhYmE1MTA3NWIyNzE1M2Q2ZGFjYmVkMDI4NzA3) * [Galaxy tips and tricks](https://github.com/bgruening/galaxy-tricks) * [Galaxy training network](http://training.galaxyproject.org) @@ -53,15 +58,15 @@ Fri | Advanced Galaxy features, discussions, bring your own data. to perform the analysis. Participants from the MPI Freiburg, please note that the European Galaxy server is different from the MPI Galaxy server. You will need to have an account on [https://usegalaxy.eu](https://usegalaxy.eu]) as well. -2. For the workshop, all you need is a computer with a latest web browser. -3. Galaxy interactive tours guide you stepwise through the Galaxy user interface +2. Please join the [slack channel](https://app.slack.com/accept-shared-channel/T032SC3N5GE/I0319JJBQHZ/enQtMzA0MzYzMDM5ODYxMS05NTViYTcyODUxZGUxZmY0N2QwMGY2NGE3YzA4YmMwOTMwNGNhYmE1MTA3NWIyNzE1M2Q2ZGFjYmVkMDI4NzA3) for discussions. +3. For the workshop, all you need is a computer with a latest web browser. +4. Galaxy interactive tours guide you stepwise through the Galaxy user interface and the history. They will help you to follow the Galaxy introduction, and ensure everyone has a basic understanding of how Galaxy works. It is recommended to go through the following two Galaxy interactive tours before beginning the training, but it is not mandatory. - -- [Galaxy UI](https://usegalaxy.eu/tours/core.galaxy_ui) -- [History Introduction](https://usegalaxy.eu/tours/core.history) + - [Galaxy UI](https://usegalaxy.eu/tours/core.galaxy_ui) + - [History Introduction](https://usegalaxy.eu/tours/core.history) If you have any questions, please do not hesitate to [contact us](mailto:contact@usegalaxy.eu). From d6a7c9055142ec40fe1a6be31ba795a4f1413b8b Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Mon, 14 Feb 2022 20:32:54 +0100 Subject: [PATCH 9/9] Remove zoom link --- _events/2021-12-23-GalaxyWS_SFB.md | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/_events/2021-12-23-GalaxyWS_SFB.md b/_events/2021-12-23-GalaxyWS_SFB.md index 28e994b8a..13ee4be11 100644 --- a/_events/2021-12-23-GalaxyWS_SFB.md +++ b/_events/2021-12-23-GalaxyWS_SFB.md @@ -23,7 +23,7 @@ online course and is limited to the members CRC 1425, CRC 992 and MeInBio. ## Venue -[Online](https://usegalaxy.eu/join-training/fr-feb-2022) +Online ## Program @@ -41,24 +41,30 @@ Thu | RNA-Seq data analysis part II Fri | Advanced Galaxy features, discussions, bring your own data. {:.table.table-striped} +### Agenda +Each day is divided in to 3 sessions: +* **Training session** is a zoom meeting where tutors will present the basic idea of the topic and demonstrate the data analysis on Galaxy and explain each analysis step. It is a popcorn session. Participants should relax and watch, ask questions but don't touch the keyboard. +* **Hands-on session** is the work-session. Participants will perform the analysis that they have learned during the training session. The training material and supporting hands-on videos are provided. All the questions during the hands-on session will be answered by the tutors in a slack channel. All the workshop information, training material and tutorial videos will stay online even after the workshop. +* **Q&A session**: Day ends with an extended live discussion on zoom where we all can discuss any remaining questions about the topic. This session will start at 16:30. + ## Links -* Zoom meeting room for Galaxy traning and Q&A sessions: [https://uni-freiburg.zoom.us/j/62060189065?pwd=Vmg4MElrWkl4M2xyLy9lSGY2bm9nUT09](https://uni-freiburg.zoom.us/j/62060189065?pwd=Vmg4MElrWkl4M2xyLy9lSGY2bm9nUT09) - - Topic: Galaxy Workshop February 2022 - - Meeting ID: 620 6018 9065 - - Passcode: aPE9j8WXi -* Slack channel for discussions during the hands-on: [link](https://app.slack.com/accept-shared-channel/T032SC3N5GE/I0319JJBQHZ/enQtMzA0MzYzMDM5ODYxMS05NTViYTcyODUxZGUxZmY0N2QwMGY2NGE3YzA4YmMwOTMwNGNhYmE1MTA3NWIyNzE1M2Q2ZGFjYmVkMDI4NzA3) +* Slack channel for discussions during the hands-on: [link](https://app.slack.com/client/T01EL3YJPC2/C031N6QA6P3) * [Galaxy tips and tricks](https://github.com/bgruening/galaxy-tricks) * [Galaxy training network](http://training.galaxyproject.org) ## Preparation +Some important steps to consider before joining the workshop: 1. Please create an account in the [European Galaxy server](https://usegalaxy.eu) to perform the analysis. Participants from the MPI Freiburg, please note that the European Galaxy server is different from the MPI Galaxy server. You will need to have an account on [https://usegalaxy.eu](https://usegalaxy.eu]) as well. -2. Please join the [slack channel](https://app.slack.com/accept-shared-channel/T032SC3N5GE/I0319JJBQHZ/enQtMzA0MzYzMDM5ODYxMS05NTViYTcyODUxZGUxZmY0N2QwMGY2NGE3YzA4YmMwOTMwNGNhYmE1MTA3NWIyNzE1M2Q2ZGFjYmVkMDI4NzA3) for discussions. +2. We use Slack for the discussions during the hands-on session. Please follow these two steps in order to join us in Slack: + - First, please register at the Galaxy training network Slack space: [https://join.slack.com/t/gtnsmrgsbord/shared_invite/zt-x7vinbs1-BA~Kht6N86JBhDq0uTIVdQ](https://join.slack.com/t/gtnsmrgsbord/shared_invite/zt-x7vinbs1-BA~Kht6N86JBhDq0uTIVdQ) + - Once you are in, join our workshop channel named freiburg-galaxy-workshop-2022 by following this link: [https://app.slack.com/client/T01EL3YJPC2/C031N6QA6P3](https://app.slack.com/client/T01EL3YJPC2/C031N6QA6P3) + - Finally, feel free to say hello to other participants. 3. For the workshop, all you need is a computer with a latest web browser. 4. Galaxy interactive tours guide you stepwise through the Galaxy user interface and the history. They will help you to follow the Galaxy introduction, and