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@@ -41,27 +41,38 @@ Thu | RNA-Seq data analysis part II | |
| Fri | Advanced Galaxy features, discussions, bring your own data. | ||
| {:.table.table-striped} | ||
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| ### 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. | ||
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| ## Links | ||
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| * 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) | ||
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| ## Preparation | ||
| Some important steps to consider before joining the workshop: | ||
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| 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. 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. 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 | ||
| 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. | ||
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| - [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) | ||
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| If you have any questions, please do not hesitate to [contact us](mailto:[email protected]). | ||
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| --- | ||
| 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/) | ||
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| ## Variant Calling | ||
|
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||
| - 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) | ||
|
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| ## 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) | ||
|
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| ## Metagenomic Analysis | ||
|
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||
| - lotus2 was updated to [6e9fd3e0dcbb](https://toolshed.g2.bx.psu.edu/view/earlhaminst/lotus2/6e9fd3e0dcbb) | ||
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| ## Annotation | ||
|
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| - interproscan was updated to [c55643c3d813](https://toolshed.g2.bx.psu.edu/view/bgruening/interproscan/c55643c3d813) | ||
|
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| ## deepTools | ||
|
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||
| - 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) | ||
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|
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|---|---|---|
| @@ -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/) | ||
|
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| ## Variant Calling | ||
|
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||
| - 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) | ||
|
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| ## Metagenomic Analysis | ||
|
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||
| - 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) | ||
|
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| ## Graph/Display Data | ||
|
|
||
| - pygenometracks was updated to [a1abfa420d9d](https://toolshed.g2.bx.psu.edu/view/iuc/pygenometracks/a1abfa420d9d) | ||
|
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| ## Assembly | ||
|
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| - hifiasm was updated to [5bec28269d95](https://toolshed.g2.bx.psu.edu/view/bgruening/hifiasm/5bec28269d95) | ||
|
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| ## Phylogenetics | ||
|
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| - pangolin was updated to [2fa9d4f1b48f](https://toolshed.g2.bx.psu.edu/view/iuc/pangolin/2fa9d4f1b48f) | ||
|
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| ## 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) | ||
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