diff options
| author |   Justin Lecher <jlec@gentoo.org> | 2017-04-30 11:12:48 +0100 |
|---|---|---|
| committer | Justin Lecher <jlec@gentoo.org> | 2017-04-30 11:12:48 +0100 |
| commit | 3199ec7737e923dc19479e5de7b31bb583071931 (patch) | |
| tree | ac5f7a0fcd510c0ee74177bc13b7211bffc8ce64 /sci-biology | |
| parent | Update local USE description (diff) | |
| download | sci-3199ec7737e923dc19479e5de7b31bb583071931.tar.gz sci-3199ec7737e923dc19479e5de7b31bb583071931.tar.bz2 sci-3199ec7737e923dc19479e5de7b31bb583071931.zip | |
Cleanup remote IDs
Signed-off-by: Justin Lecher <jlec@gentoo.org>
Diffstat (limited to 'sci-biology')
104 files changed, 122 insertions, 141 deletions
diff --git a/sci-biology/AlignGraph/metadata.xml b/sci-biology/AlignGraph/metadata.xml index f060cdca7..7863f973a 100644 --- a/sci-biology/AlignGraph/metadata.xml +++ b/sci-biology/AlignGraph/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/Atlas2/metadata.xml b/sci-biology/Atlas2/metadata.xml index 3ff6ceef1..4338746db 100644 --- a/sci-biology/Atlas2/metadata.xml +++ b/sci-biology/Atlas2/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -13,7 +13,7 @@ Atlas2 is a next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole - Exome Capture Sequencing (WECS) data. + Exome Capture Sequencing (WECS) data. </longdescription> <upstream> <remote-id type="sourceforge">downloads</remote-id> diff --git a/sci-biology/BBmap/metadata.xml b/sci-biology/BBmap/metadata.xml index 40ba306f4..75990319d 100644 --- a/sci-biology/BBmap/metadata.xml +++ b/sci-biology/BBmap/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/BRANCH/metadata.xml b/sci-biology/BRANCH/metadata.xml index e6ac3bb3f..ab90aa364 100644 --- a/sci-biology/BRANCH/metadata.xml +++ b/sci-biology/BRANCH/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/BamView/metadata.xml b/sci-biology/BamView/metadata.xml index e25129704..ecc16433b 100644 --- a/sci-biology/BamView/metadata.xml +++ b/sci-biology/BamView/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/BlastToSam/metadata.xml b/sci-biology/BlastToSam/metadata.xml index 9885a3a72..86bbb3764 100644 --- a/sci-biology/BlastToSam/metadata.xml +++ b/sci-biology/BlastToSam/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/EBARDenovo/metadata.xml b/sci-biology/EBARDenovo/metadata.xml index 3aa5ff5d7..d0f646374 100644 --- a/sci-biology/EBARDenovo/metadata.xml +++ b/sci-biology/EBARDenovo/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">ebardenovo</remote-id> + <remote-id type="sourceforge">downloads</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/FLASH/metadata.xml b/sci-biology/FLASH/metadata.xml index bb87910ab..d0f646374 100644 --- a/sci-biology/FLASH/metadata.xml +++ b/sci-biology/FLASH/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">flashpage</remote-id> + <remote-id type="sourceforge">downloads</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml index a51edc8ae..b08ab454b 100644 --- a/sci-biology/HTSeq/metadata.xml +++ b/sci-biology/HTSeq/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/IMAGE/metadata.xml b/sci-biology/IMAGE/metadata.xml index 6d3e53e2e..3dcd782d1 100644 --- a/sci-biology/IMAGE/metadata.xml +++ b/sci-biology/IMAGE/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/InterMine/metadata.xml b/sci-biology/InterMine/metadata.xml index 5ac633a2e..5c9c50b32 100644 --- a/sci-biology/InterMine/metadata.xml +++ b/sci-biology/InterMine/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/MeV/metadata.xml b/sci-biology/MeV/metadata.xml index ef6150af4..6ed96d4bc 100644 --- a/sci-biology/MeV/metadata.xml +++ b/sci-biology/MeV/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,6 +9,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">mev-tm4</remote-id> + <remote-id type="sourceforge">downloads</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/NGSTools/metadata.xml b/sci-biology/NGSTools/metadata.xml index 7361e7654..fe6859dd7 100644 --- a/sci-biology/NGSTools/metadata.xml +++ b/sci-biology/NGSTools/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/OBO-Edit/metadata.xml b/sci-biology/OBO-Edit/metadata.xml index acbbc35a4..115a34c41 100644 --- a/sci-biology/OBO-Edit/metadata.xml +++ b/sci-biology/OBO-Edit/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/RSeQC/metadata.xml b/sci-biology/RSeQC/metadata.xml index 0452b2835..54bdfb597 100644 --- a/sci-biology/RSeQC/metadata.xml +++ b/sci-biology/RSeQC/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/Ray/metadata.xml b/sci-biology/Ray/metadata.xml index 982286fb0..fb7092ff7 100644 --- a/sci-biology/Ray/metadata.xml +++ b/sci-biology/Ray/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml index 68af3388c..f053775b5 100644 --- a/sci-biology/STAR/metadata.xml +++ b/sci-biology/STAR/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/SolexaQA/metadata.xml b/sci-biology/SolexaQA/metadata.xml index c9f605e75..f7714240a 100644 --- a/sci-biology/SolexaQA/metadata.xml +++ b/sci-biology/SolexaQA/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">clview</remote-id> + <remote-id type="sourceforge">solexaqa</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/TransDecoder/metadata.xml b/sci-biology/TransDecoder/metadata.xml index 42a56a27e..1a522bbe1 100644 --- a/sci-biology/TransDecoder/metadata.xml +++ b/sci-biology/TransDecoder/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -11,6 +11,5 @@ </maintainer> <upstream> <remote-id type="github">TransDecoder/TransDecoder</remote-id> - <remote-id type="sourceforge">transdecoder</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/Trinotate/metadata.xml b/sci-biology/Trinotate/metadata.xml index f409887af..b183ac8ee 100644 --- a/sci-biology/Trinotate/metadata.xml +++ b/sci-biology/Trinotate/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/VarScan-bin/metadata.xml b/sci-biology/VarScan-bin/metadata.xml index e27dba2e9..01850f614 100644 --- a/sci-biology/VarScan-bin/metadata.xml +++ b/sci-biology/VarScan-bin/metadata.xml @@ -6,7 +6,6 @@ <name>Gentoo Science Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">varscan</remote-id> <remote-id type="github">dkoboldt/varscan</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/VarScan/metadata.xml b/sci-biology/VarScan/metadata.xml index e27dba2e9..c9cbb67e6 100644 --- a/sci-biology/VarScan/metadata.xml +++ b/sci-biology/VarScan/metadata.xml @@ -6,7 +6,7 @@ <name>Gentoo Science Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">varscan</remote-id> <remote-id type="github">dkoboldt/varscan</remote-id> + <remote-id type="sourceforge">varscan</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/abacas/metadata.xml b/sci-biology/abacas/metadata.xml index c458ee97f..d0f646374 100644 --- a/sci-biology/abacas/metadata.xml +++ b/sci-biology/abacas/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">abacas</remote-id> + <remote-id type="sourceforge">downloads</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml index d8574e5f0..5b2ca1a74 100644 --- a/sci-biology/amos/metadata.xml +++ b/sci-biology/amos/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/bambus/metadata.xml b/sci-biology/bambus/metadata.xml index 4736dbff7..1054fc1ed 100644 --- a/sci-biology/bambus/metadata.xml +++ b/sci-biology/bambus/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -11,6 +11,6 @@ </maintainer> <longdescription>Bambus is the first general purpose scaffolder that is publicly available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.</longdescription> <upstream> - <remote-id type="sourceforge">amos</remote-id> + <remote-id type="sourceforge">mira-assembler</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml index fb098c773..7f0271ab3 100644 --- a/sci-biology/bamtools/metadata.xml +++ b/sci-biology/bamtools/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml index 74c17a114..d65c87aa3 100644 --- a/sci-biology/bcftools/metadata.xml +++ b/sci-biology/bcftools/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/biobambam/metadata.xml b/sci-biology/biobambam/metadata.xml index a3e55a407..38f3b45cf 100644 --- a/sci-biology/biobambam/metadata.xml +++ b/sci-biology/biobambam/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -14,7 +14,7 @@ bammaskflags: reads BAM and writes BAM while masking (removing) bits from the fl bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. bamsort: reads BAM and writes BAM resorted by coordinates or query name bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name -</longdescription> + </longdescription> <upstream> <remote-id type="github">gt1/biobambam</remote-id> </upstream> diff --git a/sci-biology/biobambam2/metadata.xml b/sci-biology/biobambam2/metadata.xml index a3e55a407..cb036d969 100644 --- a/sci-biology/biobambam2/metadata.xml +++ b/sci-biology/biobambam2/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -14,8 +14,8 @@ bammaskflags: reads BAM and writes BAM while masking (removing) bits from the fl bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. bamsort: reads BAM and writes BAM resorted by coordinates or query name bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name -</longdescription> + </longdescription> <upstream> - <remote-id type="github">gt1/biobambam</remote-id> + <remote-id type="github">gt1/biobambam2</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/bru2nii/metadata.xml b/sci-biology/bru2nii/metadata.xml index 0cec33715..90ef9367d 100644 --- a/sci-biology/bru2nii/metadata.xml +++ b/sci-biology/bru2nii/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -8,7 +8,7 @@ <longdescription lang="en"> This is a simple tool for converting Bruker ParaVision MRI data to the NIfTI file format. It includes both a drag-and-drop graphical - interface (Bru2Nii) as well as a command line tool (Bru2). + interface (Bru2Nii) as well as a command line tool (Bru2). </longdescription> <upstream> <remote-id type="github">neurolabusc/Bru2Nii</remote-id> diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml index 0a7390bf1..8cdea5d5a 100644 --- a/sci-biology/bx-python/metadata.xml +++ b/sci-biology/bx-python/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,7 +10,7 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="pypi">bx-python</remote-id> <remote-id type="bitbucket">james_taylor/bx-python</remote-id> + <remote-id type="pypi">bx-python</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml index 1f3b07521..7f866330d 100644 --- a/sci-biology/cd-hit/metadata.xml +++ b/sci-biology/cd-hit/metadata.xml @@ -21,7 +21,6 @@ duplicates from pyrosequencing reads. The usage of other programs and scripts can be found in CD-HIT user's guide. </longdescription> <upstream> - <remote-id type="google-code">cdhit</remote-id> <remote-id type="github">weizhongli/cdhit</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/clview/metadata.xml b/sci-biology/clview/metadata.xml index 7adf609cd..31020917d 100644 --- a/sci-biology/clview/metadata.xml +++ b/sci-biology/clview/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/codonw/metadata.xml b/sci-biology/codonw/metadata.xml index f66d7b796..fcb129873 100644 --- a/sci-biology/codonw/metadata.xml +++ b/sci-biology/codonw/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/conifer/metadata.xml b/sci-biology/conifer/metadata.xml index fe4173913..d0f646374 100644 --- a/sci-biology/conifer/metadata.xml +++ b/sci-biology/conifer/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/cortex_var/metadata.xml b/sci-biology/cortex_var/metadata.xml index aeef1bbec..fe8a20d2e 100644 --- a/sci-biology/cortex_var/metadata.xml +++ b/sci-biology/cortex_var/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml index d432ff9a4..b6f11bf51 100644 --- a/sci-biology/cutadapt/metadata.xml +++ b/sci-biology/cutadapt/metadata.xml @@ -10,7 +10,7 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="pypi">cutadapt</remote-id> <remote-id type="github">marcelm/cutadapt</remote-id> + <remote-id type="pypi">cutadapt</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/dipy/metadata.xml b/sci-biology/dipy/metadata.xml index 1df8ab815..23f050681 100644 --- a/sci-biology/dipy/metadata.xml +++ b/sci-biology/dipy/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml index bab24b6a0..1055813e9 100644 --- a/sci-biology/discrover/metadata.xml +++ b/sci-biology/discrover/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/epga/metadata.xml b/sci-biology/epga/metadata.xml index 991e17bf8..615525179 100644 --- a/sci-biology/epga/metadata.xml +++ b/sci-biology/epga/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/estscan/metadata.xml b/sci-biology/estscan/metadata.xml index d709341c0..138f8c095 100644 --- a/sci-biology/estscan/metadata.xml +++ b/sci-biology/estscan/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -14,6 +14,6 @@ <flag name="ifc">Undocumented USE</flag> </use> <upstream> - <remote-id type="sourceforge">estscan</remote-id> + <remote-id type="sourceforge">downloads</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/exonerate-gff3/metadata.xml b/sci-biology/exonerate-gff3/metadata.xml index 10ca6b365..378558dab 100644 --- a/sci-biology/exonerate-gff3/metadata.xml +++ b/sci-biology/exonerate-gff3/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/fastx_toolkit/metadata.xml b/sci-biology/fastx_toolkit/metadata.xml index 8203c3958..4db9d1693 100644 --- a/sci-biology/fastx_toolkit/metadata.xml +++ b/sci-biology/fastx_toolkit/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/ffindex/metadata.xml b/sci-biology/ffindex/metadata.xml index ccb4049fc..18e09466d 100644 --- a/sci-biology/ffindex/metadata.xml +++ b/sci-biology/ffindex/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,7 +9,4 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> - <upstream> - <remote-id type="github">TransDecoder/TransDecoder</remote-id> - </upstream> </pkgmetadata> diff --git a/sci-biology/flexbar/metadata.xml b/sci-biology/flexbar/metadata.xml index 6bf81a0d4..adfdd237a 100644 --- a/sci-biology/flexbar/metadata.xml +++ b/sci-biology/flexbar/metadata.xml @@ -10,7 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">flexbar</remote-id> <remote-id type="github">seqan/flexbar</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/freebayes/metadata.xml b/sci-biology/freebayes/metadata.xml index a82cda59f..fdd189bd5 100644 --- a/sci-biology/freebayes/metadata.xml +++ b/sci-biology/freebayes/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/fsa/metadata.xml b/sci-biology/fsa/metadata.xml index ec2601d87..d0f646374 100644 --- a/sci-biology/fsa/metadata.xml +++ b/sci-biology/fsa/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">fsa</remote-id> + <remote-id type="sourceforge">downloads</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/full_lengther_next/metadata.xml b/sci-biology/full_lengther_next/metadata.xml index 5c826014b..18e09466d 100644 --- a/sci-biology/full_lengther_next/metadata.xml +++ b/sci-biology/full_lengther_next/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,7 +9,4 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> - <upstream> - <remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id> - </upstream> </pkgmetadata> diff --git a/sci-biology/gap2caf/metadata.xml b/sci-biology/gap2caf/metadata.xml index fe4173913..d0f646374 100644 --- a/sci-biology/gap2caf/metadata.xml +++ b/sci-biology/gap2caf/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml index 8c1bb6577..baaa7e21c 100644 --- a/sci-biology/gatk/metadata.xml +++ b/sci-biology/gatk/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/genomeview-bin/metadata.xml b/sci-biology/genomeview-bin/metadata.xml index b6476ca7b..6646b4398 100644 --- a/sci-biology/genomeview-bin/metadata.xml +++ b/sci-biology/genomeview-bin/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">genomeview</remote-id> + <remote-id type="sourceforge">downloads</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/gffutils/metadata.xml b/sci-biology/gffutils/metadata.xml index 70c98005f..154685621 100644 --- a/sci-biology/gffutils/metadata.xml +++ b/sci-biology/gffutils/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/glean/metadata.xml b/sci-biology/glean/metadata.xml index be2ebce92..d0f646374 100644 --- a/sci-biology/glean/metadata.xml +++ b/sci-biology/glean/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">glean-gene</remote-id> + <remote-id type="sourceforge">downloads</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/igv/metadata.xml b/sci-biology/igv/metadata.xml index 661a0adce..94761dc0e 100644 --- a/sci-biology/igv/metadata.xml +++ b/sci-biology/igv/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/jtreeview/metadata.xml b/sci-biology/jtreeview/metadata.xml index a7083bff9..8dddf1715 100644 --- a/sci-biology/jtreeview/metadata.xml +++ b/sci-biology/jtreeview/metadata.xml @@ -10,7 +10,7 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">jtreeview</remote-id> <remote-id type="bitbucket">TreeView3Dev/treeview3</remote-id> + <remote-id type="sourceforge">jtreeview</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/khmer/metadata.xml b/sci-biology/khmer/metadata.xml index 54fa7d5e4..7587454ae 100644 --- a/sci-biology/khmer/metadata.xml +++ b/sci-biology/khmer/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,7 +10,7 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="pypi">khmer</remote-id> <remote-id type="github">ged-lab/khmer</remote-id> + <remote-id type="pypi">khmer</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/lighter/metadata.xml b/sci-biology/lighter/metadata.xml index 6299d4cb3..ac43ed281 100644 --- a/sci-biology/lighter/metadata.xml +++ b/sci-biology/lighter/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/lucy/metadata.xml b/sci-biology/lucy/metadata.xml index 4aca9ee62..b349fc682 100644 --- a/sci-biology/lucy/metadata.xml +++ b/sci-biology/lucy/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/manatee-igs/metadata.xml b/sci-biology/manatee-igs/metadata.xml index 8c0eb332c..0318851d4 100644 --- a/sci-biology/manatee-igs/metadata.xml +++ b/sci-biology/manatee-igs/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/manatee-jcvi/metadata.xml b/sci-biology/manatee-jcvi/metadata.xml index 8c0eb332c..d0f646374 100644 --- a/sci-biology/manatee-jcvi/metadata.xml +++ b/sci-biology/manatee-jcvi/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">manatee</remote-id> + <remote-id type="sourceforge">downloads</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/metaseq/metadata.xml b/sci-biology/metaseq/metadata.xml index 146972acc..2e63b6ca2 100644 --- a/sci-biology/metaseq/metadata.xml +++ b/sci-biology/metaseq/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/minced/metadata.xml b/sci-biology/minced/metadata.xml index 58a5e2987..6b04ebb8e 100644 --- a/sci-biology/minced/metadata.xml +++ b/sci-biology/minced/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="github">ctSkennerton/minced/tree/master</remote-id> + <remote-id type="github">ctSkennerton/minced</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml index 0704cef48..737f0bbc5 100644 --- a/sci-biology/mira/metadata.xml +++ b/sci-biology/mira/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/mne-python/metadata.xml b/sci-biology/mne-python/metadata.xml index f1ce8eff1..8b53ad0cd 100644 --- a/sci-biology/mne-python/metadata.xml +++ b/sci-biology/mne-python/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/mrfast/metadata.xml b/sci-biology/mrfast/metadata.xml index 3d6ede5a4..cf3225665 100644 --- a/sci-biology/mrfast/metadata.xml +++ b/sci-biology/mrfast/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/mrsfast/metadata.xml b/sci-biology/mrsfast/metadata.xml index e27afbabf..07ae0c655 100644 --- a/sci-biology/mrsfast/metadata.xml +++ b/sci-biology/mrsfast/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/ncbi-genome-download/metadata.xml b/sci-biology/ncbi-genome-download/metadata.xml index 80cc5d483..da3901ed3 100644 --- a/sci-biology/ncbi-genome-download/metadata.xml +++ b/sci-biology/ncbi-genome-download/metadata.xml @@ -1,12 +1,12 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> <email>freeh4cker@gmail.com</email> <name>Bertrand Néron</name> </maintainer> - <longdescription>Scripts to download genomes from the NCBI FTP servers.</longdescription> + <longdescription>Scripts to download genomes from the NCBI FTP servers.</longdescription> <upstream> - <remote-id type="github">ncbi-genome-download</remote-id> + <remote-id type="github">kblin/ncbi-genome-download</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/ngsview/metadata.xml b/sci-biology/ngsview/metadata.xml index de315fd15..e8c46ee7f 100644 --- a/sci-biology/ngsview/metadata.xml +++ b/sci-biology/ngsview/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">ngsview</remote-id> + <remote-id type="sourceforge">projects</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/nilearn/metadata.xml b/sci-biology/nilearn/metadata.xml index 3954d1f57..2730ad207 100644 --- a/sci-biology/nilearn/metadata.xml +++ b/sci-biology/nilearn/metadata.xml @@ -18,7 +18,7 @@ <flag name="plot">Adds optional dependency needed for plotting function subset.</flag> </use> <upstream> - <remote-id type="pypi">nilearn</remote-id> <remote-id type="github">nilearn/nilearn</remote-id> + <remote-id type="pypi">nilearn</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/nitime/metadata.xml b/sci-biology/nitime/metadata.xml index 549788bdf..1ed613b50 100644 --- a/sci-biology/nitime/metadata.xml +++ b/sci-biology/nitime/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/parafly/metadata.xml b/sci-biology/parafly/metadata.xml index 6f6587b8c..f818cb27f 100644 --- a/sci-biology/parafly/metadata.xml +++ b/sci-biology/parafly/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/pb-honey/metadata.xml b/sci-biology/pb-honey/metadata.xml index 7b4669b4b..69f227c89 100644 --- a/sci-biology/pb-honey/metadata.xml +++ b/sci-biology/pb-honey/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/pb-jelly/metadata.xml b/sci-biology/pb-jelly/metadata.xml index 7b4669b4b..69f227c89 100644 --- a/sci-biology/pb-jelly/metadata.xml +++ b/sci-biology/pb-jelly/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/perlprimer/metadata.xml b/sci-biology/perlprimer/metadata.xml index 9454a7f64..63c8e8be8 100644 --- a/sci-biology/perlprimer/metadata.xml +++ b/sci-biology/perlprimer/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml index 4ec209225..c316dd522 100644 --- a/sci-biology/picard/metadata.xml +++ b/sci-biology/picard/metadata.xml @@ -10,7 +10,7 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">picard</remote-id> <remote-id type="github">broadinstitute/picard</remote-id> + <remote-id type="sourceforge">picard</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/psychopy/metadata.xml b/sci-biology/psychopy/metadata.xml index e5d49f5cb..e15c9ad62 100644 --- a/sci-biology/psychopy/metadata.xml +++ b/sci-biology/psychopy/metadata.xml @@ -6,7 +6,6 @@ <name>Horea Christian</name> </maintainer> <upstream> - <remote-id type="sourceforge">psychpy</remote-id> <remote-id type="github">psychopy/psychopy</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/pybedtools/metadata.xml b/sci-biology/pybedtools/metadata.xml index 320a73b8e..1e65e6b61 100644 --- a/sci-biology/pybedtools/metadata.xml +++ b/sci-biology/pybedtools/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/pyfaidx/metadata.xml b/sci-biology/pyfaidx/metadata.xml index ea3df526e..d12d54610 100644 --- a/sci-biology/pyfaidx/metadata.xml +++ b/sci-biology/pyfaidx/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml index d286c313f..3ff9cd0b0 100644 --- a/sci-biology/pysam/metadata.xml +++ b/sci-biology/pysam/metadata.xml @@ -1,12 +1,8 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> - <upstream> - <remote-id type="google-code">pysam</remote-id> - <remote-id type="github">pysam-developers/pysam</remote-id> - </upstream> </pkgmetadata> diff --git a/sci-biology/pysurfer/metadata.xml b/sci-biology/pysurfer/metadata.xml index 20bf7714c..35df4a292 100644 --- a/sci-biology/pysurfer/metadata.xml +++ b/sci-biology/pysurfer/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/quast/metadata.xml b/sci-biology/quast/metadata.xml index fc50a9a26..c275f1f78 100644 --- a/sci-biology/quast/metadata.xml +++ b/sci-biology/quast/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/rum/metadata.xml b/sci-biology/rum/metadata.xml index 797ed0b85..d2d1746d2 100644 --- a/sci-biology/rum/metadata.xml +++ b/sci-biology/rum/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="github">itmat/rum/wiki</remote-id> + <remote-id type="github">itmat/rum</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/sabre/metadata.xml b/sci-biology/sabre/metadata.xml index 6efd5bbbd..4e02c2f05 100644 --- a/sci-biology/sabre/metadata.xml +++ b/sci-biology/sabre/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/sailfish/metadata.xml b/sci-biology/sailfish/metadata.xml index 2831ceb14..61d2e7a64 100644 --- a/sci-biology/sailfish/metadata.xml +++ b/sci-biology/sailfish/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/salmon/metadata.xml index cb020ecde..62715bec6 100644 --- a/sci-biology/salmon/metadata.xml +++ b/sci-biology/salmon/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/samstat/metadata.xml b/sci-biology/samstat/metadata.xml index 74a00f598..516373ad8 100644 --- a/sci-biology/samstat/metadata.xml +++ b/sci-biology/samstat/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml index 5b953af48..49735ee17 100644 --- a/sci-biology/samtools/metadata.xml +++ b/sci-biology/samtools/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/scaffold_builder/metadata.xml b/sci-biology/scaffold_builder/metadata.xml index 0af91617e..d0f646374 100644 --- a/sci-biology/scaffold_builder/metadata.xml +++ b/sci-biology/scaffold_builder/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">scaffold-b</remote-id> + <remote-id type="sourceforge">downloads</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/scbi_blast/metadata.xml b/sci-biology/scbi_blast/metadata.xml index dd1623955..9eed61d49 100644 --- a/sci-biology/scbi_blast/metadata.xml +++ b/sci-biology/scbi_blast/metadata.xml @@ -10,7 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id> <remote-id type="rubygems">scbi_blast</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/scbi_fasta/metadata.xml b/sci-biology/scbi_fasta/metadata.xml index f8f3e47a2..36ecf15ef 100644 --- a/sci-biology/scbi_fasta/metadata.xml +++ b/sci-biology/scbi_fasta/metadata.xml @@ -10,7 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id> <remote-id type="rubygems">scbi_fasta</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/scbi_mapreduce/metadata.xml b/sci-biology/scbi_mapreduce/metadata.xml index a39eed183..c9e61f5f3 100644 --- a/sci-biology/scbi_mapreduce/metadata.xml +++ b/sci-biology/scbi_mapreduce/metadata.xml @@ -10,7 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id> <remote-id type="rubygems">scbi_mapreduce</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/scbi_plot/metadata.xml b/sci-biology/scbi_plot/metadata.xml index 5e2713549..4c8659f89 100644 --- a/sci-biology/scbi_plot/metadata.xml +++ b/sci-biology/scbi_plot/metadata.xml @@ -10,7 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id> <remote-id type="rubygems">scbi_plot</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/screed/metadata.xml b/sci-biology/screed/metadata.xml index 65a0f9813..21ae0b4b6 100644 --- a/sci-biology/screed/metadata.xml +++ b/sci-biology/screed/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -6,7 +6,7 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="pypi">screed</remote-id> <remote-id type="github">ged-lab/screed</remote-id> + <remote-id type="pypi">screed</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/scythe/metadata.xml b/sci-biology/scythe/metadata.xml index 09173eedf..4bcbeeb31 100644 --- a/sci-biology/scythe/metadata.xml +++ b/sci-biology/scythe/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/sga/metadata.xml b/sci-biology/sga/metadata.xml index 891445344..028b21c5d 100644 --- a/sci-biology/sga/metadata.xml +++ b/sci-biology/sga/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/sickle/metadata.xml b/sci-biology/sickle/metadata.xml index 3bf94ce42..5607edcbd 100644 --- a/sci-biology/sickle/metadata.xml +++ b/sci-biology/sickle/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/skewer-bin/metadata.xml b/sci-biology/skewer-bin/metadata.xml index ef427fa2c..4c94908e8 100644 --- a/sci-biology/skewer-bin/metadata.xml +++ b/sci-biology/skewer-bin/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/staden/metadata.xml b/sci-biology/staden/metadata.xml index 495d3ba4e..73d16b005 100644 --- a/sci-biology/staden/metadata.xml +++ b/sci-biology/staden/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/subread/metadata.xml b/sci-biology/subread/metadata.xml index 8e4c81897..dc7a68adc 100644 --- a/sci-biology/subread/metadata.xml +++ b/sci-biology/subread/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/swissknife/metadata.xml b/sci-biology/swissknife/metadata.xml index e3353da6f..cc4d8f93e 100644 --- a/sci-biology/swissknife/metadata.xml +++ b/sci-biology/swissknife/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/trinityrnaseq/metadata.xml b/sci-biology/trinityrnaseq/metadata.xml index 5c826014b..bc150ff20 100644 --- a/sci-biology/trinityrnaseq/metadata.xml +++ b/sci-biology/trinityrnaseq/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> diff --git a/sci-biology/trowel/metadata.xml b/sci-biology/trowel/metadata.xml index 111e2c698..d0f646374 100644 --- a/sci-biology/trowel/metadata.xml +++ b/sci-biology/trowel/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">trowel-ec</remote-id> + <remote-id type="sourceforge">downloads</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml index 6c22d1920..87e26a1d6 100644 --- a/sci-biology/vcftools/metadata.xml +++ b/sci-biology/vcftools/metadata.xml @@ -6,7 +6,7 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">vcftools</remote-id> <remote-id type="github">vcftools/vcftools</remote-id> + <remote-id type="sourceforge">vcftools</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml index fa8a259ff..5564097a7 100644 --- a/sci-biology/wgs-assembler/metadata.xml +++ b/sci-biology/wgs-assembler/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> |