diff --git a/files/repeatexplorer-elixir.cerit-sc.cz/README b/files/repeatexplorer-elixir.cerit-sc.cz/README deleted file mode 100644 index 3093fe5..0000000 --- a/files/repeatexplorer-elixir.cerit-sc.cz/README +++ /dev/null @@ -1,118 +0,0 @@ -# usegalaxy - -Simple galaxy installation steps. - -On fresh install of ubuntu: -``` -sudo apt-get update -sudo apt-get upgrade -y -sudo apt update -sudo apt upgrade -y -sudo apt install -y software-properties-common -sudo apt-add-repository --yes --update ppa:ansible/ansible -sudo apt install -y ansible -``` - -Clone the repo and instal required galaxy roles. -``` -git clone https://github.com/CESNET/usegalaxy.git -cd usegalaxy -ansible-galaxy install -p roles -r requirements.yml -``` -Note that the roles are already present in this repo. - -After the instalation, you should configure your [inventory file](https://training.galaxyproject.org/training-material/topics/admin/tutorials/ansible/tutorial.html#inventory-file) ([hosts](https://github.com/CESNET/usegalaxy/blob/main/hosts)) and set up a vault: -``` -openssl rand -base64 24 > .vault-password.txt -ansible-vault create group_vars/secret.yml -``` -The second command opens an editor wherein you should define variables eg.: -``` -vault_id_secret: "a-long-random-value" -rabbitmq_users_password: - mqadmin: "a-long-random-value" - galaxy: "a-long-random-value" - galaxy_gpu: "a-long-random-value" -``` -The value should be a long random value, which can be obtained by command `openssl rand -base64 24`, though you should avoid having a `/` or `\` in your password as galaxy will interpret this as a path. - -Make sure you have these ports enabled on your machine: -``` -80(HTTP) -443(HTTPS) -4369(TCP) -5671(TCP) -15672(TCP) -25672(TCP) -``` - -Once everything have been installed and configured, the ansible playbook can be run as follows: -``` -ansible-playbook galaxy.yml -``` - -## Usegalaxy tools - -Install ephemeris for tool management: -``` -virtualenv -p python3 ~/ephemeris_venv -. ~/ephemeris_venv/bin/activate -pip install ephemeris -``` -To obtain the list of tools from the [usegalaxy.eu](https://usegalaxy.eu) use: -``` -get-tool-list -g "https://usegalaxy.eu" -o "eu_tool_list.yaml" -``` -and then to install them: -``` -shed-tools install -g https://your-galaxy -a -t eu_tool_list.yaml -``` -The api key can be found in the User -> Preferences -> Manage API Key in Galaxy menu. - -... - -Later we should use this [role](https://github.com/galaxyproject/ansible-galaxy-tools) to automate this, but there are too many tools to be installed and it is very inpractical for testing purposes. - -## Debian 11 - -### TUS - -On ubuntu < 22.04 and Debian < 12 the GLIBC version is incompatible with the ```galaxyproject.tusd``` GLIBC, therfore playbook ends in error. -- in `roles/galaxyproject.tusd/defaults/main.yml` you have to set the `tusd_version:` to 'v1.8.0' (tested, possibly higher) - -### Ansible - -On Debian 11 the default version of `ansible` is 2.10.08 which fails to extract binaries for TUSd. -- workaround: - - because of Puppet, we need to create dedicated sources.list file for ansible - - `sudo vim /etc/apt/sources.list.d/ansible_ubuntu_focal_main.list` add this line : `deb http://ppa.launchpad.net/ansible/ansible/ubuntu focal main` - - then `sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 93C4A3FD7BB9C367` - - followed by `sudo apt-get update` and `sudo apt-get install ansible -y` -- Note that you might need to `sudo apt remove ansible` `sudo apt autoremove` before you try to install ansible. - -### Nginx Upload Module - -Our playbook makes use of `nginx-upload-module`, which is not included by default in any nginx-* distribution from `apt`. -This is a simple recipe for installing nginx with the upload-module. - -``` -sudo apt remove *nginx* -y && -sudo apt autoremove -y && - -wget http://nginx.org/download/nginx-1.24.0.tar.gz && -tar -xzf nginx-1.24.0.tar.gz && -cd nginx-1.24.0/ && -git clone https://github.com/hongzhidao/nginx-upload-module.git && -sudo apt-get install -y libpcre3 libpcre3-dev libssl-dev zlib1g-dev && -./configure --user=nginx --group=nginx --prefix=/etc/nginx --conf-path=/etc/nginx/nginx.conf --sbin-path=/usr/sbin/nginx --http-log-path=/var/log/nginx/access.log --error-log-path=/var/log/nginx/error.log --lock-path=/var/lock/nginx.lock --pid-path=/run/nginx.pid --modules-path=/usr/lib/nginx/modules --http-client-body-temp-path=/var/lib/nginx/body --http-fastcgi-temp-path=/var/lib/nginx/fastcgi --http-proxy-temp-path=/var/lib/nginx/proxy --http-scgi-temp-path=/var/lib/nginx/scgi --http-uwsgi-temp-path=/var/lib/nginx/uwsgi --with-compat --with-debug --with-pcre-jit --with-http_ssl_module --with-http_stub_status_module --with-http_realip_module --with-http_auth_request_module --with-http_v2_module --with-http_dav_module --with-http_slice_module --with-threads --with-http_addition_module --with-http_gunzip_module --with-http_gzip_static_module --with-http_sub_module --add-module=nginx-upload-module && -make && make install -``` - -Note that you might need to `sudo systemctl unmask nginx.service` and remove the `galaxy` and `redirect-ssl` from `/etc/nginx/sites-available and `/etc/nginx/sites-enabled` before running the playbook again. - -### Other issues - - -For influxdb apt key error: https://www.influxdata.com/blog/linux-package-signing-key-rotation/ - -For proftpd add "LoadModule mod_tls.c" to roles/galaxyproject.proftpd/templates/tls.conf.j2 just before the TLSEngine diff --git a/files/repeatexplorer-elixir.cerit-sc.cz/regalaxy_integrated_tool_panel.xml.backup b/files/repeatexplorer-elixir.cerit-sc.cz/regalaxy_integrated_tool_panel.xml.backup deleted file mode 100644 index b7565fc..0000000 --- a/files/repeatexplorer-elixir.cerit-sc.cz/regalaxy_integrated_tool_panel.xml.backup +++ /dev/null @@ -1,334 +0,0 @@ - - - -
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- diff --git a/files/repeatexplorer-elixir.cerit-sc.cz/tpv_rules_local.real.yml b/files/repeatexplorer-elixir.cerit-sc.cz/tpv_rules_local.real.yml deleted file mode 100644 index 1b30607..0000000 --- a/files/repeatexplorer-elixir.cerit-sc.cz/tpv_rules_local.real.yml +++ /dev/null @@ -1,474 +0,0 @@ -global: - default_inherits: default - -tools: - default: - abstract: true - cores: 2 - mem: 10 - env: - # Ensuring a consistent collation environment is good for reproducibility. - LC_ALL: C - GALAXY_SLOTS: "{cores}" - GALAXY_MEMORY_MB: "{int(mem)*1000}" - context: - scratch: 15 - walltime: 24 - queue: galaxyre - scheduling: - require: - - pulsar - reject: - - offline - - # Tools for testing and playing - testing.*: - cores: 1 - mem: 1 - context: - scratch: 1 - walltime: 1 - - # DANTE_TIR toolset: https://toolshed.g2.bx.psu.edu/repos/petr-novak/dante_tir - toolshed.g2.bx.psu.edu/repos/petr-novak/dante_tir/.*: - cores: 20 - mem: 32 - - # DANTE toolset: https://toolshed.g2.bx.psu.edu/repos/petr-novak/dante - toolshed.g2.bx.psu.edu/repos/petr-novak/dante/domains_filter/.*: - cores: 2 - mem: 25 - context: - scratch: 15 - toolshed.g2.bx.psu.edu/repos/petr-novak/dante/gff_to_tabular/.*: - cores: 2 - mem: 25 - context: - scratch: 15 - toolshed.g2.bx.psu.edu/repos/petr-novak/dante/gff_summary/.*: - cores: 2 - mem: 25 - context: - scratch: 15 - toolshed.g2.bx.psu.edu/repos/petr-novak/dante/domains_extract/.*: - cores: 2 - mem: 25 - context: - scratch: 15 - toolshed.g2.bx.psu.edu/repos/petr-novak/dante/dante/.*: - cores: 32 - mem: 25 - context: - scratch: 15 - walltime: 336 - - # TideCluster tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster - toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster/tidecluster_annotation/.*: - cores: 16 - mem: 24 - context: - scratch: 15 - toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster/tc_reannotate/.*: - cores: 32 - mem: 50 - context: - scratch: 15 - walltime: 96 - toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster/tidecluster/.*: - cores: 16 - mem: 64 - context: - scratch: 150 - walltime: 336 - - # repeat_annotation_pipeline tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3 - toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/extract_re_contigs/.*: - cores: 2 - mem: 10 - context: - scratch: 15 - toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/compare_gff/.*: - cores: 2 - mem: 10 - context: - scratch: 15 - toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/summarize_gff_by_attribute/.*: - cores: 2 - mem: 10 - context: - scratch: 15 - toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/annotate_contigs/.*: - cores: 2 - mem: 10 - context: - scratch: 15 - toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/repeat_annotate/.*: - cores: 32 - mem: 50 - context: - scratch: 50 - walltime: 96 - - # re_utils tools https://toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/RMsearch2/.*: - cores: 16 - mem: 32 - context: - scratch: 50 - walltime: 96 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/chip_seq_ratio_1/.*: - cores: 16 - mem: 32 - context: - scratch: 50 - walltime: 48 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/rename_sequences/.*: - cores: 2 - mem: 10 - context: - scratch: 50 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/pairScan/.*: - cores: 2 - mem: 10 - context: - scratch: 50 - walltime: 48 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/single_fastq_filtering/.*: - cores: 6 - mem: 10 - context: - scratch: 50 - walltime: 24 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/fasta_affixer/.*: - cores: 2 - mem: 10 - context: - scratch: 50 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/sampler/.*: - cores: 2 - mem: 10 - context: - scratch: 15 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/plot_comparative/.*: - cores: 2 - mem: 10 - context: - scratch: 15 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/extract_var_files_from_re/.*: - cores: 2 - mem: 10 - context: - scratch: 50 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/summarize_annotation/.*: - cores: 2 - mem: 10 - context: - scratch: 50 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/names_affixer/.*: - cores: 2 - mem: 10 - context: - scratch: 50 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/cluster_table2krona_format/.*: - cores: 2 - mem: 10 - context: - scratch: 50 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/fasta_input/.*: - cores: 2 - mem: 10 - context: - scratch: 50 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/fasta_interlacer/.*: - cores: 2 - mem: 10 - context: - scratch: 50 - toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/paired_fastq_filtering/.*: -# cores: 6 #DEMON: old setting but seems pointless - cores: 2 -# mem: 10 #DEMON: old setting but there was job which used 78GB; the best would be to scale to input size - mem: 50 - context: - scratch: 50 -# walltime: 24 #DEMON: used to be 24h but if input is very big it could take more time, would be great to scale it to input size - walltime: 48 - - # DANTE_ltr tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr - toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/dante_ltr_summary/.*: - cores: 2 - mem: 10 - context: - scratch: 15 - toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/clean_dante_ltr/.*: - cores: 32 - mem: 64 - context: - scratch: 64 - walltime: 168 - toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/dante_ltr_search/.*: - cores: 32 - mem: 64 - context: - scratch: 64 - walltime: 168 - toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/dante_ltr_to_library/.*: - cores: 32 - mem: 64 - context: - scratch: 64 - walltime: 168 - - # ReapeatExplorer tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing - toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing/repeatexplorer2/.*: - cores: 10 - mem: 4 - context: - scratch: 50 - walltime: 48 - scheduling: - require: - - pulsar - - singularity - container_resolvers: - - type: cached_explicit_singularity - cache_directory: "$SINGULARITY_CACHEDIR" - - type: explicit_singularity - - type: cached_mulled_singularity - cache_directory: "$SINGULARITY_CACHEDIR" - - auto_install: true - type: mulled_singularity - - auto_install: false - cache_directory: /mnt/galaxy-re/singularity/mulled - type: build_mulled_singularity - params: - singularity_default_container_id: "/storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/singularity_cache/cache/library/sha256.660dda926394f3db2400f7800e064cf731c75566853cac43a30be44e3b5f5d73" - rules: - - id: queue_definition_by_parameter - if: | - param_dict = job.get_param_values(app) # get job input parameters as dictionary - 'queue_definition' in param_dict and 'queue_specification' in param_dict['queue_definition'] - cores: | - import re - int(re.search(r'ncpus=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) - mem: | - import re - int(re.search(r'mem=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) - context: - scratch: | - import re - int(re.search(r'scratch_local=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) - walltime: | - import re - int(re.search(r'walltime=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) - - id: basic_fast_queue_selected - if: | - param_dict = job.get_param_values(app) # get job input parameters as dictionary - 'queue_select' in param_dict and param_dict['queue_select'].startswith('basic_fast_queue') - cores: 10 - mem: 16 - context: - scratch: 50 - walltime: 48 - - id: long_slow_queue_selected - if: | - param_dict = job.get_param_values(app) # get job input parameters as dictionary - 'queue_select' in param_dict and param_dict['queue_select'].startswith('long_slow_queue') - cores: 16 - mem: 64 - context: - scratch: 50 - walltime: 336 - - id: extra_long_slow_queue_selected - if: | - param_dict = job.get_param_values(app) # get job input parameters as dictionary - 'queue_select' in param_dict and param_dict['queue_select'].startswith('extra_long_slow_queue') - cores: 16 - mem: 64 - context: - scratch: 50 - walltime: 720 - - toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing/tarean/.*: - inherits: toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing/repeatexplorer2/.* - - .*/fastq_groomer/.*: - cores: 1 - mem: 16 - -roles: - training.*: - max_cores: 2 - max_mem: "int(max_cores * 3.8)" - scheduling: - require: - - training - helper: - scheduling: - require: - - helper - highmem: - mem: 512 - context: - queue: elixircz - test: - scheduling: - require: - - test - -destinations: - tpv_local: - runner: local_runner - max_accepted_cores: 1 - max_accepted_mem: 4 - params: - tmp_dir: true - scheduling: - require: - - local - reject: - - singularity - tpv_local_singularity: - runner: local_runner - max_accepted_cores: 1 - max_accepted_mem: 4 - params: - singularity_enabled: true - singularity_default_container_id: "/cvmfs/singularity.galaxyproject.org/all/python:3.8.3" - env: - SINGULARITY_CACHEDIR: "/mnt/galaxy-re/singularity/" - SINGULARITY_TMPDIR: /mnt/galaxy-re/tmp - scheduling: - require: - - local - prefer: - - singularity - tpv_pulsar: - runner: pulsar_runner - max_accepted_cores: 32 - max_accepted_mem: 185 - max_accepted_gpus: 0 - max_cores: 32 - max_mem: 128 - max_gpus: 0 - params: - default_file_action: remote_rsync_transfer - transport: rsync - ssh_user: "galaxyelixir" - ssh_host: "repeatexplorer-elixir.cerit-sc.cz" - ssh_port: 22 - ssh_key: | - -----BEGIN OPENSSH PRIVATE KEY----- - b3BlbnNzaC1rZXktdjEAAAAABG5vbmUAAAAEbm9uZQAAAAAAAAABAAAAMwAAAAtzc2gtZW - QyNTUxOQAAACDyeKTY+KWQX5v4Rkg9OGZLsbQm2oHjccEg+hAGfsMo0AAAAKgS5zlWEuc5 - VgAAAAtzc2gtZWQyNTUxOQAAACDyeKTY+KWQX5v4Rkg9OGZLsbQm2oHjccEg+hAGfsMo0A - AAAECe7yi98nsOset8Jo7V2Gmh19TtINb+4Cnx8YFxJSgKafJ4pNj4pZBfm/hGSD04Zkux - tCbageNxwSD6EAZ+wyjQAAAAJWdhbGF4eWVsaXhpckBnYWxheHktcmUuZ3JpZC5jZXNuZX - QuY3o= - -----END OPENSSH PRIVATE KEY----- - dependency_resolution: remote - jobs_directory: /storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/staging - persistence_directory: /opt/pulsar/files/persistent - remote_metadata: false - rewrite_parameters: true - outputs_to_working_directory: false - submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue}@pbs-m1.metacentrum.cz -N pulsar_re_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" - env: - TMPDIR: $SCRATCHDIR - TMP: $SCRATCHDIR - TEMP: $SCRATCHDIR - scheduling: - require: - - pulsar - reject: - - singularity - tpv_pulsar_singularity: - inherits: tpv_pulsar - runner: pulsar_runner - params: - singularity_enabled: true - singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR:rw" - singularity_default_container_id: "/cvmfs/singularity.galaxyproject.org/all/python:3.8.3" - submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue}@pbs-m1.metacentrum.cz -N pulsar_re_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" - env: - SINGULARITY_CACHEDIR: "/storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/singularity_cache" - SINGULARITY_TMPDIR: "$SCRATCHDIR" - XDG_CACHE_HOME: "$SCRATCHDIR" - scheduling: - require: - - pulsar - - singularity - tpv_pulsar_test: - inherits: tpv_pulsar - runner: pulsar_runner - params: - submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue}@pbs-m1.metacentrum.cz -N pulsar_re_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" - scheduling: - require: - - pulsar - - test - reject: - - singularity - tpv_pulsar_highmem: - inherits: tpv_pulsar - runner: pulsar_runner - max_accepted_mem: 512 - max_mem: 512 - - tpv_pulsar_helper: - runner: pulsar_helper - max_accepted_cores: 32 - max_accepted_mem: 185 - max_accepted_gpus: 0 - max_cores: 32 - max_mem: 128 - max_gpus: 0 - params: - default_file_action: remote_rsync_transfer - transport: rsync - ssh_user: "galaxyelixir" - ssh_host: "repeatexplorer-elixir.cerit-sc.cz" - ssh_port: 22 - ssh_key: | - -----BEGIN OPENSSH PRIVATE KEY----- - b3BlbnNzaC1rZXktdjEAAAAABG5vbmUAAAAEbm9uZQAAAAAAAAABAAAAMwAAAAtzc2gtZW - QyNTUxOQAAACDyeKTY+KWQX5v4Rkg9OGZLsbQm2oHjccEg+hAGfsMo0AAAAKgS5zlWEuc5 - VgAAAAtzc2gtZWQyNTUxOQAAACDyeKTY+KWQX5v4Rkg9OGZLsbQm2oHjccEg+hAGfsMo0A - AAAECe7yi98nsOset8Jo7V2Gmh19TtINb+4Cnx8YFxJSgKafJ4pNj4pZBfm/hGSD04Zkux - tCbageNxwSD6EAZ+wyjQAAAAJWdhbGF4eWVsaXhpckBnYWxheHktcmUuZ3JpZC5jZXNuZX - QuY3o= - -----END OPENSSH PRIVATE KEY----- - dependency_resolution: remote - jobs_directory: /storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/staging - persistence_directory: /opt/pulsar/files/persistent - remote_metadata: false - rewrite_parameters: true - outputs_to_working_directory: false - submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue}@pbs-m1.metacentrum.cz -N pulsar_re_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" - env: - TMPDIR: $SCRATCHDIR - TMP: $SCRATCHDIR - TEMP: $SCRATCHDIR - scheduling: - require: - - pulsar - - helper - reject: - - singularity - tpv_pulsar_singularity_helper: - inherits: tpv_pulsar_helper - runner: pulsar_helper - params: - singularity_enabled: true - singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR:rw" - singularity_default_container_id: "/cvmfs/singularity.galaxyproject.org/all/python:3.8.3" - submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue}@pbs-m1.metacentrum.cz -N pulsar_re_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" - env: - SINGULARITY_CACHEDIR: "/storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/singularity_cache" - SINGULARITY_TMPDIR: "$SCRATCHDIR" - XDG_CACHE_HOME: "$SCRATCHDIR" - scheduling: - require: - - pulsar - - helper - - singularity