| Previous changeset 10:9dc43bf7d1db (2018-06-01) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty" |
|
modified:
align_families.xml correct_barcodes.xml dunovo.xml make_families.xml precheck.xml |
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added:
err.log err2.log out.log out2.log |
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removed:
tool_dependencies.xml |
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| diff -r 9dc43bf7d1db -r 0f8e0dc73d1d align_families.xml --- a/align_families.xml Fri Jun 01 17:55:23 2018 -0400 +++ b/align_families.xml Wed Feb 16 22:59:00 2022 +0000 |
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| @@ -1,10 +1,8 @@ <?xml version="1.0"?> -<tool id="align_families" name="Du Novo: Align families" version="2.15"> +<tool id="align_families" name="Du Novo: Align families" version="3.0.2"> <description>of duplex sequencing reads</description> <requirements> - <requirement type="package" version="7.221">mafft</requirement> - <requirement type="package" version="2.15">dunovo</requirement> - <!-- TODO: require Python 2.7 --> + <requirement type="package" version="3.0.2">dunovo</requirement> </requirements> <version_command>align-families.py --version</version_command> <command detect_errors="exit_code">align-families.py $check_ids --aligner $aligner --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' > '$output' @@ -28,6 +26,7 @@ </test> <test> <param name="input" value="families.sort.tsv"/> + <param name="check_ids" value="--no-check-ids"/> <output name="output" file="families.msa.tsv"/> </test> </tests> |
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| diff -r 9dc43bf7d1db -r 0f8e0dc73d1d correct_barcodes.xml --- a/correct_barcodes.xml Fri Jun 01 17:55:23 2018 -0400 +++ b/correct_barcodes.xml Wed Feb 16 22:59:00 2022 +0000 |
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| @@ -1,16 +1,17 @@ <?xml version="1.0"?> -<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.15"> +<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="3.0.2"> <description>of duplex sequencing reads</description> <requirements> - <requirement type="package" version="1.1.2">bowtie</requirement> - <requirement type="package" version="1.10">networkx</requirement> - <requirement type="package" version="2.15">dunovo</requirement> - <!-- TODO: require Python 2.7 --> + <requirement type="package" version="3.0.2">dunovo</requirement> </requirements> <version_command>correct.py --version</version_command> <command detect_errors="exit_code"><![CDATA[ - baralign.sh -c $advanced.chunkmbs -t \${GALAXY_SLOTS:-1} '$input' refdir correct.sam - && correct.py --galaxy $phone $check_ids --dist $dist --mapq $mapq --pos $pos + baralign.sh -c $advanced.chunkmbs -t \${GALAXY_SLOTS:-1} -g + #if $phone == '--phone-home': + -p + #end if + '$input' refdir correct.sam + && correct.py --galaxy $phone $check_ids $allow_no_nm_if_ns --dist $dist --mapq $mapq --pos $pos '$input' refdir/barcodes.fa correct.sam > families.corrected.tsv && sort families.corrected.tsv @@ -19,11 +20,12 @@ </command> <inputs> <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> - <param name="dist" type="integer" value="3" min="1" label="Maximum differences" help="Only use alignments where the barcodes differ by at most these many errors. Note that raising this beyond 3 probably won't have an effect, because of the inherent limit in bowtie's ability to match up distant barcodes."/> + <param name="dist" type="integer" value="3" min="1" label="Maximum differences" help="Only use alignments where the barcodes differ by at most these many errors. Note that raising this beyond 3 won't have an effect, because of the inherent limit in bowtie's ability to match up distant barcodes."/> <param name="mapq" type="integer" value="20" min="0" label="Minimum mapping quality" help="Only use alignments whose MAPQ is at least this."/> <param name="pos" type="integer" value="2" min="0" label="Maximum start offset" help="Ignore alignments where the start positions differ by more than this."/> <param name="check_ids" type="boolean" truevalue="" falsevalue="--no-check-ids" checked="True" label="Check read names" help="Make sure reads are properly paired up. The job will fail if there is a pair of reads where their ids aren't identical (minus any ending /1 or /2)."/> - <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the time and memory taken to process it, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The parameters and input/output dataset names are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET"/> + <param name="allow_no_nm_if_ns" type="boolean" truevalue="--allow-no-nm-if-ns" falsevalue="" checked="False" label="Allow missing NM tags" help="Allow alignments with missing NM tags if the barcode has at least one N. Try checking this if you get the error "Alignment missing NM tag, but likely due to N's in sequence"."/> + <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the time and memory taken to process it, some performance-related parameters, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The parameters and input/output dataset names are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET"/> <section name="advanced" title="Advanced Options" expanded="false"> <param name="chunkmbs" type="integer" value="512" min="16" label="bowtie --chunkmbs" help="This is the number of megabytes to give each bowtie thread for storing path descriptors. If you see warnings about "Exhausted best-first chunk memory" in stderr, you need to increase this."/> </section> |
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| diff -r 9dc43bf7d1db -r 0f8e0dc73d1d dunovo.xml --- a/dunovo.xml Fri Jun 01 17:55:23 2018 -0400 +++ b/dunovo.xml Wed Feb 16 22:59:00 2022 +0000 |
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| @@ -1,9 +1,8 @@ <?xml version="1.0"?> -<tool id="dunovo" name="Du Novo: Make consensus reads" version="2.15"> +<tool id="dunovo" name="Du Novo: Make consensus reads" version="3.0.2"> <description>from duplex sequencing alignments</description> <requirements> - <requirement type="package" version="2.15">dunovo</requirement> - <!-- TODO: require Python 2.7 --> + <requirement type="package" version="3.0.2">dunovo</requirement> </requirements> <version_command>make-consensi.py --version</version_command> <command detect_errors="exit_code"> @@ -11,16 +10,21 @@ #if $out_format.type == 'fastq': --fastq-out $out_format.qual #end if - --qual $qual_thres --qual-format $qual_format --min-reads $min_reads --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2' + --aligner $advanced.aligner --qual $qual_thres --qual-format $qual_format --min-reads $min_reads --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2' #if $keep_sscs: --sscs1 '$sscs1' --sscs2 '$sscs2' #end if </command> <inputs> <param name="input" type="data" format="tabular" label="Aligned input reads" /> - <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads for a consensus" help="This many reads are necessary to form a single-strand consensus sequence. Families smaller than this will be skipped."/> - <param name="cons_thres" type="float" value="0.5" min="0.5" max="1.0" label="Consensus % threshold" help="The consensus base must be present in more than this fraction of the reads, or "N" will be used instead."/> - <param name="min_cons_reads" type="integer" value="0" min="0" label="Minimum number of reads for a consensus base." help="The consensus base must be present in more than this absolute number of reads, or "N" will be used instead."/> + <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads for a consensus" help="This many reads are necessary to form a single-strand consensus sequence. Families smaller than this will be skipped and no consensus (single or duplex) will be produced."/> + <param name="cons_thres" type="float" value="0.7" min="0" max="1.0" label="Consensus % threshold" help="Each consensus base must be present in more than this fraction of the reads, or "N" will be used instead."/> + <param name="min_cons_reads" type="integer" value="0" min="0" label="Minimum number of reads for a consensus base." help="Each consensus base must be present in more than this absolute number of reads, or "N" will be used instead. The "Consensus % threshold" sets a threshold based on the number of reads in the family, while this threshold is a fixed, absolute number. If both are used, the consensus base must pass both requirements."/> + <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/> + <param name="qual_format" type="select" label="Input quality score format" help="Format of the FASTQ files of the raw reads. Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+"> + <option value="sanger" selected="true">Sanger (PHRED 0 = "!")</option> + <option value="solexa">Solexa (PHRED 0 = "@")</option> + </param> <conditional name="out_format"> <param name="type" type="select" label="Output format"> <option value="fasta" selected="true">FASTA</option> @@ -30,13 +34,14 @@ <param name="qual" type="integer" value="40" min="0" max="93" label="Output PHRED score" help="There is currently no way to output a meaningful quality score for consensus bases. You'll have to specify an artificial one, which will be given to every base. A good value is 40, the maximum score normally output by sequencers. This means the bases won't be inadvertently filtered out by some downstream tool."/> </when> </conditional> - <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/> - <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+"> - <option value="sanger" selected="true">Sanger (PHRED 0 = "!")</option> - <option value="solexa">Solexa (PHRED 0 = "@")</option> - </param> <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" /> <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the number of processes used, the time and memory taken to process it, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The parameters and input/output dataset names are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET."/> + <section name="advanced" title="Advanced Options" expanded="false"> + <param name="aligner" type="select" value="biopython" label="Pairwise sequence aligner" help="Which pairwise alignment library to use. "BioPython" uses BioPython's PairwiseAligner and a substitution matrix built by Bioconductor's Biostrings package. "swalign" is a custom Smith-Waterman implementation by Nicolaus Lance Hepler. It is deprecated and kept only for backward compatibility."> + <option value="biopython">BioPython</option> + <option value="swalign">swalign</option> + </param> + </section> </inputs> <outputs> <data name="dcs1" label="$tool.name on $on_string (mate 1)"> |
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| diff -r 9dc43bf7d1db -r 0f8e0dc73d1d err.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/err.log Wed Feb 16 22:59:00 2022 +0000 |
| [ |
| b'@@ -0,0 +1,728 @@\n+planemo couldn\'t find a target test-data directory, you should likely create a test-data directory or pass an explicit path using --test_data.\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Cloning into \'/tmp/tmppmuqm8bo/galaxy-dev\'...\n+done.\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.0"\n+warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^3.4.2"\n+warning Resolution field "ua-parser-js@0.7.30" is incompatible with requested version "ua-parser-js@0.7.22"\n+warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8"\n+warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.4"\n+warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8"\n+warning "@galaxyproject/bootstrap-tour > bootstrap@5.0.2" has unmet peer dependency "@popperjs/core@^2.9.2".\n+warning " > @handsontable/vue@2.0.0" has incorrect peer dependency "handsontable@^4.0.0".\n+warning " > @hirez_io/observer-spy@2.0.0" has unmet peer dependency "typescript@>=2.8.1".\n+warning " > linkifyjs@2.1.9" has unmet peer dependency "react@>= 0.14.0".\n+warning " > linkifyjs@2.1.9" has unmet peer dependency "react-dom@>= 0.14.0".\n+warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.\n+warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the \'parcel\' package. See https://v2.parceljs.org/getting-started/migration for details.\n+warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.\n+warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies\n+warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.\n+warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.\n+warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.\n+warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142\n+warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142\n+warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated\n+warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.\n+warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142\n+warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer sup'..b'ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140222822082304 and this is thread id 140224748214080.\n+[2022-02-16 16:21:36 -0500] [2610616] [INFO] Shutting down: Master\n+Traceback (most recent call last):\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 665, in _config_directory\n+ yield config_directory\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config\n+ yield LocalGalaxyConfig(\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config\n+ yield config\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 48, in _serve\n+ exit_code = run_galaxy_command(\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/run.py", line 118, in run_galaxy_command\n+ exit_code = shell(command, env=env)\n+ File "/home/me/.local/lib/python3.8/site-packages/galaxy/util/commands.py", line 60, in shell\n+ return p.wait()\n+ File "/usr/lib/python3.8/subprocess.py", line 1083, in wait\n+ return self._wait(timeout=timeout)\n+ File "/usr/lib/python3.8/subprocess.py", line 1806, in _wait\n+ (pid, sts) = self._try_wait(0)\n+ File "/usr/lib/python3.8/subprocess.py", line 1764, in _try_wait\n+ (pid, sts) = os.waitpid(self.pid, wait_flags)\n+KeyboardInterrupt\n+\n+During handling of the above exception, another exception occurred:\n+\n+Traceback (most recent call last):\n+ File "/home/me/.local/bin/planemo", line 8, in <module>\n+ sys.exit(planemo())\n+ File "/usr/lib/python3/dist-packages/click/core.py", line 764, in __call__\n+ return self.main(*args, **kwargs)\n+ File "/usr/lib/python3/dist-packages/click/core.py", line 717, in main\n+ rv = self.invoke(ctx)\n+ File "/usr/lib/python3/dist-packages/click/core.py", line 1137, in invoke\n+ return _process_result(sub_ctx.command.invoke(sub_ctx))\n+ File "/usr/lib/python3/dist-packages/click/core.py", line 956, in invoke\n+ return ctx.invoke(self.callback, **ctx.params)\n+ File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke\n+ return callback(*args, **kwargs)\n+ File "/usr/lib/python3/dist-packages/click/decorators.py", line 64, in new_func\n+ return ctx.invoke(f, obj, *args, **kwargs)\n+ File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke\n+ return callback(*args, **kwargs)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/cli.py", line 98, in handle_blended_options\n+ return f(*args, **kwds)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/commands/cmd_serve.py", line 43, in cli\n+ galaxy_serve(ctx, runnables, **kwds)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 25, in serve\n+ return _serve(ctx, runnables, **kwds)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 72, in _serve\n+ return config\n+ File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__\n+ self.gen.throw(type, value, traceback)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config\n+ yield config\n+ File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__\n+ self.gen.throw(type, value, traceback)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config\n+ yield LocalGalaxyConfig(\n+ File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__\n+ self.gen.throw(type, value, traceback)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 669, in _config_directory\n+ shutil.rmtree(config_directory)\n+ File "/usr/lib/python3.8/shutil.py", line 722, in rmtree\n+ onerror(os.rmdir, path, sys.exc_info())\n+ File "/usr/lib/python3.8/shutil.py", line 720, in rmtree\n+ os.rmdir(path)\n+OSError: [Errno 39] Directory not empty: \'/tmp/tmppmuqm8bo\'\n' |
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| diff -r 9dc43bf7d1db -r 0f8e0dc73d1d err2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/err2.log Wed Feb 16 22:59:00 2022 +0000 |
| [ |
| b'@@ -0,0 +1,1139 @@\n+planemo couldn\'t find a target test-data directory, you should likely create a test-data directory or pass an explicit path using --test_data.\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Cloning into \'/tmp/tmp1upz926i/galaxy-dev\'...\n+done.\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.0"\n+warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^3.4.2"\n+warning Resolution field "ua-parser-js@0.7.30" is incompatible with requested version "ua-parser-js@0.7.22"\n+warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8"\n+warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.4"\n+warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8"\n+warning "@galaxyproject/bootstrap-tour > bootstrap@5.0.2" has unmet peer dependency "@popperjs/core@^2.9.2".\n+warning " > @handsontable/vue@2.0.0" has incorrect peer dependency "handsontable@^4.0.0".\n+warning " > @hirez_io/observer-spy@2.0.0" has unmet peer dependency "typescript@>=2.8.1".\n+warning " > linkifyjs@2.1.9" has unmet peer dependency "react@>= 0.14.0".\n+warning " > linkifyjs@2.1.9" has unmet peer dependency "react-dom@>= 0.14.0".\n+warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.\n+warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the \'parcel\' package. See https://v2.parceljs.org/getting-started/migration for details.\n+warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.\n+warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies\n+warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.\n+warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.\n+warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated\n+warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.\n+warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.\n+warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142\n+warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142\n+warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated\n+warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated\n+warning parcel-bundler > micromatch > snapdragon > sourc'..b'ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140196716734208 and this is thread id 140198646921024.\n+[2022-02-16 17:28:36 -0500] [2654000] [INFO] Shutting down: Master\n+Traceback (most recent call last):\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 665, in _config_directory\n+ yield config_directory\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config\n+ yield LocalGalaxyConfig(\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config\n+ yield config\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 48, in _serve\n+ exit_code = run_galaxy_command(\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/run.py", line 118, in run_galaxy_command\n+ exit_code = shell(command, env=env)\n+ File "/home/me/.local/lib/python3.8/site-packages/galaxy/util/commands.py", line 60, in shell\n+ return p.wait()\n+ File "/usr/lib/python3.8/subprocess.py", line 1083, in wait\n+ return self._wait(timeout=timeout)\n+ File "/usr/lib/python3.8/subprocess.py", line 1806, in _wait\n+ (pid, sts) = self._try_wait(0)\n+ File "/usr/lib/python3.8/subprocess.py", line 1764, in _try_wait\n+ (pid, sts) = os.waitpid(self.pid, wait_flags)\n+KeyboardInterrupt\n+\n+During handling of the above exception, another exception occurred:\n+\n+Traceback (most recent call last):\n+ File "/home/me/.local/bin/planemo", line 8, in <module>\n+ sys.exit(planemo())\n+ File "/usr/lib/python3/dist-packages/click/core.py", line 764, in __call__\n+ return self.main(*args, **kwargs)\n+ File "/usr/lib/python3/dist-packages/click/core.py", line 717, in main\n+ rv = self.invoke(ctx)\n+ File "/usr/lib/python3/dist-packages/click/core.py", line 1137, in invoke\n+ return _process_result(sub_ctx.command.invoke(sub_ctx))\n+ File "/usr/lib/python3/dist-packages/click/core.py", line 956, in invoke\n+ return ctx.invoke(self.callback, **ctx.params)\n+ File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke\n+ return callback(*args, **kwargs)\n+ File "/usr/lib/python3/dist-packages/click/decorators.py", line 64, in new_func\n+ return ctx.invoke(f, obj, *args, **kwargs)\n+ File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke\n+ return callback(*args, **kwargs)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/cli.py", line 98, in handle_blended_options\n+ return f(*args, **kwds)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/commands/cmd_serve.py", line 43, in cli\n+ galaxy_serve(ctx, runnables, **kwds)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 25, in serve\n+ return _serve(ctx, runnables, **kwds)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 72, in _serve\n+ return config\n+ File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__\n+ self.gen.throw(type, value, traceback)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config\n+ yield config\n+ File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__\n+ self.gen.throw(type, value, traceback)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config\n+ yield LocalGalaxyConfig(\n+ File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__\n+ self.gen.throw(type, value, traceback)\n+ File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 669, in _config_directory\n+ shutil.rmtree(config_directory)\n+ File "/usr/lib/python3.8/shutil.py", line 722, in rmtree\n+ onerror(os.rmdir, path, sys.exc_info())\n+ File "/usr/lib/python3.8/shutil.py", line 720, in rmtree\n+ os.rmdir(path)\n+OSError: [Errno 39] Directory not empty: \'/tmp/tmp1upz926i\'\n' |
| b |
| diff -r 9dc43bf7d1db -r 0f8e0dc73d1d make_families.xml --- a/make_families.xml Fri Jun 01 17:55:23 2018 -0400 +++ b/make_families.xml Wed Feb 16 22:59:00 2022 +0000 |
| b |
| @@ -1,10 +1,9 @@ <?xml version="1.0"?> -<tool id="make_families" name="Du Novo: Make families" version="2.15"> +<tool id="make_families" name="Du Novo: Make families" version="3.0.2"> <description>of duplex sequencing reads</description> <requirements> - <requirement type="package" version="2.15">dunovo</requirement> + <requirement type="package" version="3.0.2">dunovo</requirement> </requirements> - <!-- TODO: Add dependency on coreutils to get paste? --> <version_command>make-consensi.py --version</version_command> <command detect_errors="exit_code">make-families.sh -t $taglen -i $invariant '$fastq1' '$fastq2' > '$output' </command> @@ -21,14 +20,14 @@ <test> <param name="fastq1" value="smoke_1.fq"/> <param name="fastq2" value="smoke_2.fq"/> - <param name="taglen" value="5"/> + <param name="taglen" value="4"/> <param name="invariant" value="1"/> <output name="output" file="smoke.families.tsv"/> </test> <test> <param name="fastq1" value="smoke_1.fq"/> <param name="fastq2" value="smoke_2.fq"/> - <param name="taglen" value="5"/> + <param name="taglen" value="4"/> <param name="invariant" value="0"/> <output name="output" file="smoke.families.i0.tsv"/> </test> |
| b |
| diff -r 9dc43bf7d1db -r 0f8e0dc73d1d out.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/out.log Wed Feb 16 22:59:00 2022 +0000 |
| [ |
| b'@@ -0,0 +1,1698 @@\n+git --git-dir /home/me/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/me/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/me/.planemo/gx_repo remote update >/dev/null 2>&1\n+git clone --branch master /home/me/.planemo/gx_repo /tmp/tmppmuqm8bo/galaxy-dev\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/me/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /usr/bin/python3 -m venv $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && COMMON_STARTUP_ARGS=; $(grep -q \'skip-venv\' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+Activated a virtualenv for Galaxy\n+/home/me/.planemo/gx_venv_3\n+Set COMMON_STARTUP_ARGS to --dev-wheels\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/me/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=19.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (20.0.2)\n+Ignoring async-exit-stack: markers \'python_version >= "3.6" and python_version < "3.7"\' don\'t match your environment\n+Ignoring async-generator: markers \'python_version < "3.7" and python_version >= "3.6"\' don\'t match your environment\n+Ignoring atomicwrites: markers \'python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version < "3.8" and python_version >= "3.6"\' don\'t match your environment\n+Ignoring cffi: markers \'implementation_name == "pypy" and python_version >= "3.6" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0")\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.5.0"\' don\'t match your environment\n+Ignoring contextvars: markers \'python_version < "3.7" and python_version >= "3.6"\' don\'t match your environment\n+Ignoring dataclasses: markers \'python_version >= "3.6" and python_version < "3.7"\' don\'t match your environment\n+Ignoring immutables: markers \'python_version >= "3.6" and python_version < "3.7"\' don\'t match your environment\n+Ignoring importlib-metadata: markers \'python_version < "3.8" and python_version >= "3.6" and (python_version == "3.6" or python_version == "3.7") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.4.0" and python_version >= "3.6" and python_version < "3.8")\' don\'t match your environment\n+Ignoring importlib-resources: markers \'python_version < "3.7" and python_version >= "3.6"\' don\'t match your environment\n+Ignoring py: markers \'python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or python_full_version >= "3.4.0" and python_version >= "3.6" and implementation_name == "pypy"\' don\'t match your environment\n+Ignoring pycparser: markers \'python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or implementation_name == "pypy" and python_version >= "3.6" and python_full_version >= "3.4.0"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8"\' don\'t match your environment\n+Ignoring pyreadline: markers \'python_version >= "'..b'b3==1.26.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 250)) (1.26.4)\n+Requirement already satisfied: uvicorn==0.13.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 251)) (0.13.4)\n+Requirement already satisfied: vine==5.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 252)) (5.0.0)\n+Requirement already satisfied: watchdog==2.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 253)) (2.0.3)\n+Requirement already satisfied: wcwidth==0.2.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 254)) (0.2.5)\n+Requirement already satisfied: webencodings==0.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 255)) (0.5.1)\n+Requirement already satisfied: webob==1.8.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 256)) (1.8.7)\n+Requirement already satisfied: whoosh==2.7.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 257)) (2.7.4)\n+Requirement already satisfied: wrapt==1.12.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 258)) (1.12.1)\n+Requirement already satisfied: xmlrunner==1.7.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 259)) (1.7.7)\n+Requirement already satisfied: yacman==0.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 260)) (0.8.2)\n+Requirement already satisfied: zipstream-new==1.1.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 262)) (1.1.8)\n+Requirement already satisfied: cffi>=1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from bcrypt==3.2.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (1.15.0)\n+Requirement already satisfied: colorama>=0.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cmd2==1.5.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (0.4.4)\n+Requirement already satisfied: setuptools in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==3.0.20201109103151->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (44.0.0)\n+Requirement already satisfied: typing-extensions in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==3.0.20201109103151->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (4.1.1)\n+Requirement already satisfied: py>=1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from pytest==6.2.3->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 180)) (1.11.0)\n+Requirement already satisfied: rich>=9.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from refgenconf==0.12.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 196)) (11.2.0)\n+Requirement already satisfied: pycparser in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cffi>=1.1->bcrypt==3.2.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (2.21)\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple\n+Requirement already satisfied: watchdog in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r /dev/stdin (line 1)) (2.0.3)\n+The Galaxy client build is up to date and will not be rebuilt at this time.\n+Activating virtualenv at /home/me/.planemo/gx_venv_3\n+Executing: gunicorn --pythonpath lib --paste "/tmp/tmppmuqm8bo/galaxy.ini" \n' |
| b |
| diff -r 9dc43bf7d1db -r 0f8e0dc73d1d out2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/out2.log Wed Feb 16 22:59:00 2022 +0000 |
| [ |
| b'@@ -0,0 +1,1704 @@\n+git --git-dir /home/me/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/me/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/me/.planemo/gx_repo remote update >/dev/null 2>&1\n+git clone --branch master /home/me/.planemo/gx_repo /tmp/tmp1upz926i/galaxy-dev\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/me/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /usr/bin/python3 -m venv $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && COMMON_STARTUP_ARGS=; $(grep -q \'skip-venv\' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+Activated a virtualenv for Galaxy\n+/home/me/.planemo/gx_venv_3\n+Set COMMON_STARTUP_ARGS to --dev-wheels\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/me/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=19.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (20.0.2)\n+Ignoring async-exit-stack: markers \'python_version >= "3.6" and python_version < "3.7"\' don\'t match your environment\n+Ignoring async-generator: markers \'python_version < "3.7" and python_version >= "3.6"\' don\'t match your environment\n+Ignoring atomicwrites: markers \'python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version < "3.8" and python_version >= "3.6"\' don\'t match your environment\n+Ignoring cffi: markers \'implementation_name == "pypy" and python_version >= "3.6" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0")\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.5.0"\' don\'t match your environment\n+Ignoring contextvars: markers \'python_version < "3.7" and python_version >= "3.6"\' don\'t match your environment\n+Ignoring dataclasses: markers \'python_version >= "3.6" and python_version < "3.7"\' don\'t match your environment\n+Ignoring immutables: markers \'python_version >= "3.6" and python_version < "3.7"\' don\'t match your environment\n+Ignoring importlib-metadata: markers \'python_version < "3.8" and python_version >= "3.6" and (python_version == "3.6" or python_version == "3.7") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.4.0" and python_version >= "3.6" and python_version < "3.8")\' don\'t match your environment\n+Ignoring importlib-resources: markers \'python_version < "3.7" and python_version >= "3.6"\' don\'t match your environment\n+Ignoring py: markers \'python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or python_full_version >= "3.4.0" and python_version >= "3.6" and implementation_name == "pypy"\' don\'t match your environment\n+Ignoring pycparser: markers \'python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or implementation_name == "pypy" and python_version >= "3.6" and python_full_version >= "3.4.0"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8"\' don\'t match your environment\n+Ignoring pyreadline: markers \'python_version >= "'..b'b3==1.26.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 250)) (1.26.4)\n+Requirement already satisfied: uvicorn==0.13.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 251)) (0.13.4)\n+Requirement already satisfied: vine==5.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 252)) (5.0.0)\n+Requirement already satisfied: watchdog==2.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 253)) (2.0.3)\n+Requirement already satisfied: wcwidth==0.2.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 254)) (0.2.5)\n+Requirement already satisfied: webencodings==0.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 255)) (0.5.1)\n+Requirement already satisfied: webob==1.8.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 256)) (1.8.7)\n+Requirement already satisfied: whoosh==2.7.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 257)) (2.7.4)\n+Requirement already satisfied: wrapt==1.12.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 258)) (1.12.1)\n+Requirement already satisfied: xmlrunner==1.7.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 259)) (1.7.7)\n+Requirement already satisfied: yacman==0.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 260)) (0.8.2)\n+Requirement already satisfied: zipstream-new==1.1.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 262)) (1.1.8)\n+Requirement already satisfied: cffi>=1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from bcrypt==3.2.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (1.15.0)\n+Requirement already satisfied: colorama>=0.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cmd2==1.5.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (0.4.4)\n+Requirement already satisfied: typing-extensions in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==3.0.20201109103151->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (4.1.1)\n+Requirement already satisfied: setuptools in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==3.0.20201109103151->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (44.0.0)\n+Requirement already satisfied: py>=1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from pytest==6.2.3->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 180)) (1.11.0)\n+Requirement already satisfied: rich>=9.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from refgenconf==0.12.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 196)) (11.2.0)\n+Requirement already satisfied: pycparser in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cffi>=1.1->bcrypt==3.2.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (2.21)\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple\n+Requirement already satisfied: watchdog in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r /dev/stdin (line 1)) (2.0.3)\n+The Galaxy client build is up to date and will not be rebuilt at this time.\n+Activating virtualenv at /home/me/.planemo/gx_venv_3\n+Executing: gunicorn --pythonpath lib --paste "/tmp/tmp1upz926i/galaxy.ini" \n' |
| b |
| diff -r 9dc43bf7d1db -r 0f8e0dc73d1d precheck.xml --- a/precheck.xml Fri Jun 01 17:55:23 2018 -0400 +++ b/precheck.xml Wed Feb 16 22:59:00 2022 +0000 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> -<tool id="precheck" name="Du Novo: Check input" version="2.15"> +<tool id="precheck" name="Du Novo: Check input" version="3.0.2"> <requirements> - <requirement type="package" version="2.15">dunovo</requirement> + <requirement type="package" version="3.0.2">dunovo</requirement> </requirements> <description>for family content</description> <command detect_errors="exit_code"> |
| b |
| diff -r 9dc43bf7d1db -r 0f8e0dc73d1d tool_dependencies.xml --- a/tool_dependencies.xml Fri Jun 01 17:55:23 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,78 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bowtie" version="1.1.2"> - <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="mafft" version="7.221"> - <repository changeset_revision="c5908940967d" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="networkx" version="1.10"> - <repository changeset_revision="e761775277c1" name="package_networkx_1_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="dunovo" version="2.15"> - <install version="1.0"> - <actions> - <!-- download the main dunovo package files --> - <action sha256sum="1cf02bcc37cc641a20bdf5e20c2b3b98d4dccd43b1182830cb1a9e7d173d1a78" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.15.tar.gz</action> - <!-- TODO: Store dunovo version number in variable instead of hardcoding it everywhere. --> - <!-- install submodules --> - <action type="shell_command">rmdir kalign utillib ET</action> - <!-- download the utillib submodule --> - <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action> - <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action> - <action type="shell_command">rm v0.1.0.tar.gz</action> - <action rename_to="utillib" type="move_file"> - <source>utillib-0.1.0</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <!-- download the kalign submodule --> - <action type="download_file">https://github.com/makovalab-psu/kalign-dunovo/archive/v0.2.0.tar.gz</action> - <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action> - <action type="shell_command">rm v0.2.0.tar.gz</action> - <action rename_to="kalign" type="move_file"> - <source>kalign-dunovo-0.2.0</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <!-- download the ET submodule --> - <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action> - <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action> - <action type="shell_command">rm v0.2.2.tar.gz</action> - <action rename_to="ET" type="move_file"> - <source>ET-0.2.2</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <!-- download the bfx submodule --> - <action type="download_file">https://github.com/NickSto/bfx/archive/v0.2.0.tar.gz</action> - <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action> - <action type="shell_command">rm v0.2.0.tar.gz</action> - <action rename_to="bfx" type="move_file"> - <source>bfx-0.2.0</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <!-- Move some source files from subdirectories into the main source directory. --> - <action type="move_file"> - <source>utils/precheck.py</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <action type="move_file"> - <source>bfx/trimmer.py</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <action type="move_file"> - <source>utils/getreads.py</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <!-- make and install --> - <action type="shell_command">make clean</action> - <action type="shell_command">make</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - </package> -</tool_dependency> |