From f72c8b2447f2bc88462b48383a8148662372649a Mon Sep 17 00:00:00 2001 From: iprada Date: Mon, 3 Jun 2019 15:02:21 +0200 Subject: [PATCH 01/24] Update README.md --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index a034ce1..5aaaeb9 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,9 @@ Installation using **pip**: python -m pip install Circle-Map -Installation through conda/bioconda will be supported soon. +Installation using **conda** + + conda install -c bioconda circle-map **Note**: If you have use pip and you want to simulate circular DNA short reads, you will need to install [BBMap](https://sourceforge.net/projects/bbmap/) and [ART](https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm) on your system. From d9ab8bdd0a20263fd1fdebeacfa94cca4b5c6e13 Mon Sep 17 00:00:00 2001 From: iprada Date: Mon, 3 Jun 2019 15:02:39 +0200 Subject: [PATCH 02/24] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5aaaeb9..cc6360f 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ Installation using **pip**: python -m pip install Circle-Map -Installation using **conda** +Installation using **conda**: conda install -c bioconda circle-map From 6a0665b4992aa7a4c954b9fdb017aa54fe7ce097 Mon Sep 17 00:00:00 2001 From: iprada Date: Mon, 3 Jun 2019 18:58:47 +0200 Subject: [PATCH 03/24] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index cc6360f..b8675be 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ Installation using **conda**: Now you are ready to get started detecting circular DNA. We have created a [Circle-Map wiki](https://github.com/iprada/Circle-Map/wiki) that explains step by step how you can go from your raw sequencing reads to interpretable results. In the wiki, you can try and learn using Circle-Map with the following tutorials: - * [Tutorial: identification of mappable circular DNA using Circle Map Realign](https://github.com/iprada/Circle-Map/wiki/Tutorial:-identification-of-mappable-circular-DNA-using-Circle-Map-Realign) + * [Tutorial: identification of mappable circular DNA using Circle Map Realign](https://github.com/iprada/Circle-Map/wiki/Tutorial:-Identification-of-circular-DNA-using-Circle-Map-Realign) ## Getting help From e0ce770bec9f4299955c9ef1f30ea9774af33109 Mon Sep 17 00:00:00 2001 From: iprada Date: Tue, 4 Jun 2019 10:38:38 +0200 Subject: [PATCH 04/24] Update README.md --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index b8675be..5be8806 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,12 @@ # Welcome to Circle-Map official repository! + +https://anaconda.org/bioconda/circle-map/badges/version.svg +https://anaconda.org/bioconda/circle-map/badges/latest_release_date.svg +https://anaconda.org/bioconda/circle-map/badges/license.svg +https://anaconda.org/bioconda/circle-map/badges/downloads.svg +https://anaconda.org/bioconda/circle-map/badges/installer/conda.svg + Circle-Map is an easy to install, python package that implements all the steps required to detect extrachromosomal DNA circles. The package contains easy to run algorithms for accurately detect circular DNA formed from mappable and non mappable regions of a genome. From 1229846c1c8493989b88cac9024b76489497b73d Mon Sep 17 00:00:00 2001 From: iprada Date: Tue, 4 Jun 2019 10:41:17 +0200 Subject: [PATCH 05/24] Update README.md --- README.md | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/README.md b/README.md index 5be8806..f77bbcb 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,5 @@ # Welcome to Circle-Map official repository! - - -https://anaconda.org/bioconda/circle-map/badges/version.svg -https://anaconda.org/bioconda/circle-map/badges/latest_release_date.svg -https://anaconda.org/bioconda/circle-map/badges/license.svg -https://anaconda.org/bioconda/circle-map/badges/downloads.svg -https://anaconda.org/bioconda/circle-map/badges/installer/conda.svg +[![PyPI](https://img.shields.io/pypi/v/Circle-Map.svg)](https://pypi.python.org/pypi/Circle-Map) Circle-Map is an easy to install, python package that implements all the steps required to detect extrachromosomal DNA circles. The package contains easy to run algorithms for accurately detect circular DNA formed from mappable and non mappable regions of a genome. From 238d5eb501baf228c54410f8ee6a6865af72ffd7 Mon Sep 17 00:00:00 2001 From: iprada Date: Tue, 4 Jun 2019 10:41:26 +0200 Subject: [PATCH 06/24] Update README.md From e4f7d93d166f25d5a55804740dcb195e0c412289 Mon Sep 17 00:00:00 2001 From: iprada Date: Tue, 4 Jun 2019 10:42:11 +0200 Subject: [PATCH 07/24] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index f77bbcb..6cdbeeb 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ # Welcome to Circle-Map official repository! [![PyPI](https://img.shields.io/pypi/v/Circle-Map.svg)](https://pypi.python.org/pypi/Circle-Map) +[![Anaconda-Server Downloads](https://anaconda.org/bioconda/circele-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) Circle-Map is an easy to install, python package that implements all the steps required to detect extrachromosomal DNA circles. The package contains easy to run algorithms for accurately detect circular DNA formed from mappable and non mappable regions of a genome. From 2d970fb73c84506dfa05deba629100b681d3a57a Mon Sep 17 00:00:00 2001 From: iprada Date: Tue, 4 Jun 2019 10:42:26 +0200 Subject: [PATCH 08/24] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6cdbeeb..6ea6391 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # Welcome to Circle-Map official repository! [![PyPI](https://img.shields.io/pypi/v/Circle-Map.svg)](https://pypi.python.org/pypi/Circle-Map) -[![Anaconda-Server Downloads](https://anaconda.org/bioconda/circele-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) +[![Anaconda-Server Downloads](https://anaconda.org/bioconda/circle-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) Circle-Map is an easy to install, python package that implements all the steps required to detect extrachromosomal DNA circles. The package contains easy to run algorithms for accurately detect circular DNA formed from mappable and non mappable regions of a genome. From 4412361ec932e9e069f9a653fc75baa5d16b390c Mon Sep 17 00:00:00 2001 From: iprada Date: Tue, 4 Jun 2019 10:44:32 +0200 Subject: [PATCH 09/24] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 6ea6391..2fd5c68 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # Welcome to Circle-Map official repository! [![PyPI](https://img.shields.io/pypi/v/Circle-Map.svg)](https://pypi.python.org/pypi/Circle-Map) [![Anaconda-Server Downloads](https://anaconda.org/bioconda/circle-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) +[![GitHub Downloads](https://img.shields.io/github/downloads/iprada/Circle-Map/total.svg?style=social&logo=github&label=Download)](https://github.com/iprada/Circle-Map/releases) Circle-Map is an easy to install, python package that implements all the steps required to detect extrachromosomal DNA circles. The package contains easy to run algorithms for accurately detect circular DNA formed from mappable and non mappable regions of a genome. From 87d001af2f49ea812998da48dbde9e610ac66b07 Mon Sep 17 00:00:00 2001 From: iprada Date: Tue, 4 Jun 2019 10:47:46 +0200 Subject: [PATCH 10/24] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 2fd5c68..009f733 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ # Welcome to Circle-Map official repository! [![PyPI](https://img.shields.io/pypi/v/Circle-Map.svg)](https://pypi.python.org/pypi/Circle-Map) +[![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/version.svg)](https://anaconda.org/bioconda/circle-map) [![Anaconda-Server Downloads](https://anaconda.org/bioconda/circle-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) [![GitHub Downloads](https://img.shields.io/github/downloads/iprada/Circle-Map/total.svg?style=social&logo=github&label=Download)](https://github.com/iprada/Circle-Map/releases) From ae61ad4c1a467512714fa6d76f3b26c72a5ea20c Mon Sep 17 00:00:00 2001 From: iprada Date: Tue, 4 Jun 2019 10:48:40 +0200 Subject: [PATCH 11/24] Update README.md --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 009f733..79573ff 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,8 @@ [![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/version.svg)](https://anaconda.org/bioconda/circle-map) [![Anaconda-Server Downloads](https://anaconda.org/bioconda/circle-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) [![GitHub Downloads](https://img.shields.io/github/downloads/iprada/Circle-Map/total.svg?style=social&logo=github&label=Download)](https://github.com/iprada/Circle-Map/releases) +[![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/latest_release_date.svg)](https://anaconda.org/bioconda/circle-map) +[![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/license.svg)](https://anaconda.org/bioconda/circle-map) Circle-Map is an easy to install, python package that implements all the steps required to detect extrachromosomal DNA circles. The package contains easy to run algorithms for accurately detect circular DNA formed from mappable and non mappable regions of a genome. From 8a0d0f8ab7653f5f7815959b9f0c42b90deae32c Mon Sep 17 00:00:00 2001 From: iprada Date: Tue, 4 Jun 2019 10:49:31 +0200 Subject: [PATCH 12/24] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 79573ff..a169e93 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ [![Anaconda-Server Downloads](https://anaconda.org/bioconda/circle-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) [![GitHub Downloads](https://img.shields.io/github/downloads/iprada/Circle-Map/total.svg?style=social&logo=github&label=Download)](https://github.com/iprada/Circle-Map/releases) [![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/latest_release_date.svg)](https://anaconda.org/bioconda/circle-map) -[![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/license.svg)](https://anaconda.org/bioconda/circle-map) +[![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/license.svg)](https://github.com/iprada/Circle-Map/blob/master/LICENSE) Circle-Map is an easy to install, python package that implements all the steps required to detect extrachromosomal DNA circles. The package contains easy to run algorithms for accurately detect circular DNA formed from mappable and non mappable regions of a genome. From 6bc2af3788e85e11598fe4e68c5791ff78d2aab1 Mon Sep 17 00:00:00 2001 From: iprada Date: Tue, 4 Jun 2019 10:55:35 +0200 Subject: [PATCH 13/24] Update README.md --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index a169e93..477e1b0 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,9 @@ # Welcome to Circle-Map official repository! [![PyPI](https://img.shields.io/pypi/v/Circle-Map.svg)](https://pypi.python.org/pypi/Circle-Map) [![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/version.svg)](https://anaconda.org/bioconda/circle-map) -[![Anaconda-Server Downloads](https://anaconda.org/bioconda/circle-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) +[![Anaconda-Server bioonda Downloads](https://anaconda.org/bioconda/circle-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) [![GitHub Downloads](https://img.shields.io/github/downloads/iprada/Circle-Map/total.svg?style=social&logo=github&label=Download)](https://github.com/iprada/Circle-Map/releases) +![PyPI - Downloads](https://img.shields.io/pypi/dm/Circle-Map.svg?label=PyPI) [![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/latest_release_date.svg)](https://anaconda.org/bioconda/circle-map) [![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/license.svg)](https://github.com/iprada/Circle-Map/blob/master/LICENSE) From f3765bc9b57d221bcfcedd07010cb163741b686a Mon Sep 17 00:00:00 2001 From: iprada Date: Tue, 4 Jun 2019 11:00:37 +0200 Subject: [PATCH 14/24] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 477e1b0..bd2d108 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,9 @@ # Welcome to Circle-Map official repository! [![PyPI](https://img.shields.io/pypi/v/Circle-Map.svg)](https://pypi.python.org/pypi/Circle-Map) [![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/version.svg)](https://anaconda.org/bioconda/circle-map) -[![Anaconda-Server bioonda Downloads](https://anaconda.org/bioconda/circle-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) +[![Anaconda-Server Downloads](https://anaconda.org/bioconda/circle-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) [![GitHub Downloads](https://img.shields.io/github/downloads/iprada/Circle-Map/total.svg?style=social&logo=github&label=Download)](https://github.com/iprada/Circle-Map/releases) -![PyPI - Downloads](https://img.shields.io/pypi/dm/Circle-Map.svg?label=PyPI) +![PyPI Downloads- Downloads](https://img.shields.io/pypi/dm/Circle-Map.svg?label=PyPI) [![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/latest_release_date.svg)](https://anaconda.org/bioconda/circle-map) [![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/license.svg)](https://github.com/iprada/Circle-Map/blob/master/LICENSE) From c8edff218ed12afd75375af59181f303015c1cf4 Mon Sep 17 00:00:00 2001 From: iprada Date: Tue, 4 Jun 2019 11:01:07 +0200 Subject: [PATCH 15/24] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index bd2d108..7cc3d89 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # Welcome to Circle-Map official repository! [![PyPI](https://img.shields.io/pypi/v/Circle-Map.svg)](https://pypi.python.org/pypi/Circle-Map) [![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/version.svg)](https://anaconda.org/bioconda/circle-map) -[![Anaconda-Server Downloads](https://anaconda.org/bioconda/circle-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) +[![Bioconda Downloads](https://anaconda.org/bioconda/circle-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) [![GitHub Downloads](https://img.shields.io/github/downloads/iprada/Circle-Map/total.svg?style=social&logo=github&label=Download)](https://github.com/iprada/Circle-Map/releases) ![PyPI Downloads- Downloads](https://img.shields.io/pypi/dm/Circle-Map.svg?label=PyPI) [![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/latest_release_date.svg)](https://anaconda.org/bioconda/circle-map) From 89cd37b06438f5a24146bb34ce68b34fdb2628c6 Mon Sep 17 00:00:00 2001 From: iprada Date: Thu, 11 Jul 2019 13:43:42 +0200 Subject: [PATCH 16/24] Update README.md --- README.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 7cc3d89..5a20c65 100644 --- a/README.md +++ b/README.md @@ -41,12 +41,20 @@ Installation using **conda**: Now you are ready to get started detecting circular DNA. We have created a [Circle-Map wiki](https://github.com/iprada/Circle-Map/wiki) that explains step by step how you can go from your raw sequencing reads to interpretable results. In the wiki, you can try and learn using Circle-Map with the following tutorials: - * [Tutorial: identification of mappable circular DNA using Circle Map Realign](https://github.com/iprada/Circle-Map/wiki/Tutorial:-Identification-of-circular-DNA-using-Circle-Map-Realign) + * [Tutorial: identification of mappable circular DNA using Circle Map Realign](https://github.com/iprada/Circle-Map/wiki/Tutorial:-Identification-of-circular-DNA-using-Circle-Map-Realign) + + +Once you have detect circular DNA in your samples you will probably be interested at looking at the output files. To help you understanding the output, we have create a page explaining what is the information provided by Circle-Map in every column of its output. You can find the information in the following link: + +* [Circle-Map output explanation](https://github.com/iprada/Circle-Map/wiki/Circle-Map-output-files) + + ## Getting help The best place for getting help, feedback,report bugs or request new features is to post an [issue](https://github.com/iprada/Circle-Map/issues). You can also reach me at xsh723 at dot binf dot ku dot dk + ## Citing *Sensitive detection of circular DNA at single-nucleotide resolution using guided realignment of partially aligned reads* From b018b1bd97523d3c16161353fc765aae88c5be1c Mon Sep 17 00:00:00 2001 From: iprada Date: Thu, 11 Jul 2019 15:41:04 +0200 Subject: [PATCH 17/24] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 5a20c65..3817183 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,7 @@ Installation using **conda**: conda install -c bioconda circle-map -**Note**: If you have use pip and you want to simulate circular DNA short reads, you will need to install [BBMap](https://sourceforge.net/projects/bbmap/) and [ART](https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm) on your system. +**Note**: If you have used pip and you want to simulate circular DNA short reads, you will need to install [BBMap](https://sourceforge.net/projects/bbmap/) and [ART](https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm) on your system. ### Using Circle-Map @@ -44,7 +44,7 @@ Now you are ready to get started detecting circular DNA. We have created a [Circ * [Tutorial: identification of mappable circular DNA using Circle Map Realign](https://github.com/iprada/Circle-Map/wiki/Tutorial:-Identification-of-circular-DNA-using-Circle-Map-Realign) -Once you have detect circular DNA in your samples you will probably be interested at looking at the output files. To help you understanding the output, we have create a page explaining what is the information provided by Circle-Map in every column of its output. You can find the information in the following link: +Once you have detected circular DNA in your samples you will probably be interested at looking at the output files. To help you understanding the output, we have created a page explaining what is the information provided by Circle-Map in every column of its output. You can find the information in the following link: * [Circle-Map output explanation](https://github.com/iprada/Circle-Map/wiki/Circle-Map-output-files) From 387e13631cff4e94597698d55b967d5d52aa24a0 Mon Sep 17 00:00:00 2001 From: iprada Date: Mon, 15 Jul 2019 15:11:47 +0200 Subject: [PATCH 18/24] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3817183..2d9745f 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ Unlike other methods, Circle-Map is able to map both segments of the soft-clippe ### Installation -Circle-Map runs on GNU/Linux operating systems, and can be installed and set-up using the following ways: +Circle-Map runs on GNU/Linux operating systems,**required >=python3.6*** and can be installed and set-up using the following ways: This will install Circle-Map, and all the external packages required run every part of Circle-Map software. From 66d6ed941e183e2f4e1f9b5e057aa95547bc7756 Mon Sep 17 00:00:00 2001 From: iprada Date: Mon, 15 Jul 2019 15:12:04 +0200 Subject: [PATCH 19/24] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 2d9745f..b2395b3 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ Unlike other methods, Circle-Map is able to map both segments of the soft-clippe ### Installation -Circle-Map runs on GNU/Linux operating systems,**required >=python3.6*** and can be installed and set-up using the following ways: +Circle-Map runs on GNU/Linux operating systems,**required >=python3.6** and can be installed and set-up using the following ways: This will install Circle-Map, and all the external packages required run every part of Circle-Map software. From 504b321ee609cc6cc5a4e7a87cb6ba9e70799abf Mon Sep 17 00:00:00 2001 From: iprada Date: Mon, 15 Jul 2019 15:12:19 +0200 Subject: [PATCH 20/24] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b2395b3..8b0bf5f 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ Unlike other methods, Circle-Map is able to map both segments of the soft-clippe ### Installation -Circle-Map runs on GNU/Linux operating systems,**required >=python3.6** and can be installed and set-up using the following ways: +Circle-Map runs on GNU/Linux operating systems,**requires >=python3.6** and can be installed and set-up using the following ways: This will install Circle-Map, and all the external packages required run every part of Circle-Map software. From 1fb8e3c56d10a3263019ae2a8bf75db0c34ada03 Mon Sep 17 00:00:00 2001 From: iprada Date: Mon, 15 Jul 2019 15:12:44 +0200 Subject: [PATCH 21/24] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8b0bf5f..dbe8799 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ Unlike other methods, Circle-Map is able to map both segments of the soft-clippe ### Installation -Circle-Map runs on GNU/Linux operating systems,**requires >=python3.6** and can be installed and set-up using the following ways: +Circle-Map runs on GNU/Linux operating systems, **requires >=python3.6** and can be installed and set-up using the following ways: This will install Circle-Map, and all the external packages required run every part of Circle-Map software. From 7c0eeccb82a33b690bcac2557ade2f739d0782cb Mon Sep 17 00:00:00 2001 From: iprada Date: Thu, 18 Jul 2019 09:59:02 +0200 Subject: [PATCH 22/24] Update README.md --- README.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/README.md b/README.md index dbe8799..669d064 100644 --- a/README.md +++ b/README.md @@ -2,8 +2,6 @@ [![PyPI](https://img.shields.io/pypi/v/Circle-Map.svg)](https://pypi.python.org/pypi/Circle-Map) [![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/version.svg)](https://anaconda.org/bioconda/circle-map) [![Bioconda Downloads](https://anaconda.org/bioconda/circle-map/badges/downloads.svg)](https://anaconda.org/bioconda/circle-map) -[![GitHub Downloads](https://img.shields.io/github/downloads/iprada/Circle-Map/total.svg?style=social&logo=github&label=Download)](https://github.com/iprada/Circle-Map/releases) -![PyPI Downloads- Downloads](https://img.shields.io/pypi/dm/Circle-Map.svg?label=PyPI) [![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/latest_release_date.svg)](https://anaconda.org/bioconda/circle-map) [![Anaconda-Server Badge](https://anaconda.org/bioconda/circle-map/badges/license.svg)](https://github.com/iprada/Circle-Map/blob/master/LICENSE) From 2841e687d93069136e7551b14a4f91b84a261dfd Mon Sep 17 00:00:00 2001 From: iprada Date: Wed, 24 Jul 2019 17:21:22 +0200 Subject: [PATCH 23/24] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 669d064..e7d4ffa 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ Unlike other methods, Circle-Map is able to map both segments of the soft-clippe Circle-Map runs on GNU/Linux operating systems, **requires >=python3.6** and can be installed and set-up using the following ways: -This will install Circle-Map, and all the external packages required run every part of Circle-Map software. +This will install Circle-Map, and all the external packages required to run every part of Circle-Map software. Installation using **pip**: From 2c82dfc012966323ef5f3be3d04ad846962c18bc Mon Sep 17 00:00:00 2001 From: iprada Date: Wed, 24 Jul 2019 17:21:58 +0200 Subject: [PATCH 24/24] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e7d4ffa..360b233 100644 --- a/README.md +++ b/README.md @@ -33,7 +33,7 @@ Installation using **conda**: conda install -c bioconda circle-map -**Note**: If you have used pip and you want to simulate circular DNA short reads, you will need to install [BBMap](https://sourceforge.net/projects/bbmap/) and [ART](https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm) on your system. +**Note**: If you want to simulate circular DNA short reads, you will need to install [BBMap](https://sourceforge.net/projects/bbmap/) and [ART](https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm) on your system. ### Using Circle-Map