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Problem with downloading datasets using wget or curl

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Problem with downloading datasets using wget or curl

Ashok Varadharajan
Dear Team,

We are running galaxy-16.07 behind the proxy using nginx, uwsgi and supervisor in scientific linux 7. I have problem with downloading datasets using wget. 

I am getting the following html for all my datasets in the galaxy when I try to download it using wget [for example:  wget http://{GALAXYURL}/galaxy/datasets/xxxxxxxxxxxx/display?to_ext=tabular]

Can anyone help me to solve this issue ?


<!DOCTYPE HTML>
<html>
    <!--js-app.mako-->
    <head>
        <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
        <meta name="viewport" content="maximum-scale=1.0">
        <meta http-equiv="X-UA-Compatible" content="IE=Edge,chrome=1">
        <title>Galaxy</title>
        <link rel="index" href="/galaxy/"/>
        <link href="/galaxy/static/style/jquery.rating.css?v=1489572328" media="screen" rel="stylesheet" type="text/css" />
<link href="/galaxy/static/style/jquery-ui/smoothness/jquery-ui.css?v=1489572328" media="screen" rel="stylesheet" type="text/css" />
<link href="/galaxy/static/style/base.css?v=1489572328" media="screen" rel="stylesheet" type="text/css" />
<link href="/galaxy/static/style/bootstrap-tour.css?v=1489572328" media="screen" rel="stylesheet" type="text/css" />
    <script type="text/javascript">
        // this is needed *before* the app code is loaded - many MVC access Galaxy.root for their url
        // TODO: change this by using a common Backbone.Model base class and url fn
        window.Galaxy = { root: '/galaxy/' };
    </script>
    </head>
    <body scroll="no" class="full-content">
        <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;">
            <div id="background"></div>
            <div id="masthead" class="navbar navbar-fixed-top navbar-inverse"></div>
            <div id="messagebox" style="display: none;"></div>
            <div id="inactivebox" class="panel-warning-message" style="display: none;"></div>
        </div><!--end everything-->
        <div id='dd-helper' style="display: none;"></div>
    <noscript>
        <div class="overlay overlay-background noscript-overlay">
            <div>
                <h3 class="title">Javascript Required for Galaxy</h3>
                <div>
                    The Galaxy analysis interface requires a browser with Javascript enabled.<br>
                    Please enable Javascript and refresh this page.
                </div>
            </div>
        </div>
    </noscript>
        <script src="/galaxy/static/scripts/bundled/libs.bundled.js?v=1489572328" type="text/javascript"></script>
<script src="/galaxy/static/scripts/bundled/login.bundled.js?v=1489572328" type="text/javascript"></script>
        <script type="text/javascript">
            app(
                {"redirect": "/galaxy/datasets/xxxxxxxxxxxxxxxx/display", "show_welcome_with_login": false, "user": {"quota_percent": null, "id": null, "total_disk_usage": 0.0, "nice_total_disk_usage": "0 bytes"}, "openid_providers": [], "root": "/galaxy/", "config": {"communication_server_host": "http://localhost", "ftp_upload_site": null, "mailing_lists": "https://wiki.galaxyproject.org/MailingLists", "nginx_upload_path": "/galaxy/api/tools", "terms_url": null, "enable_unique_workflow_defaults": false, "wiki_url": "https://wiki.galaxyproject.org/", "version_major": "16.07", "support_url": "https://wiki.galaxyproject.org/Support", "persistent_communication_rooms": [], "remote_user_logout_href": null,
"message_box_content": null, "logo_src": "/galaxy/static/images/galaxyIcon_noText.png", "biostar_url_redirect": "http://{GALAXY_URL}/galaxy/biostar/biostar_redirect", "message_box_visible": false, "ftp_upload_dir": "{ftp_upload_dir}", "logo_url": "/galaxy/", "brand": "{BRAND}", "search_url": "http://galaxyproject.org/search/usegalaxy/", "screencasts_url": null, "ga_code": null, "require_login": true, "communication_server_port": 7070, "lims_doc_url": "https://usegalaxy.org/u/rkchak/p/sts", "inactivity_box_content": "Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address.", "citation_url": "https://wiki.galaxyproject.org/CitingGalaxy", "allow_user_creation": false, "is_admin_user": false, "allow_user_dataset_purge": true, "server_startttime": 1489572328,
"biostar_url": null, "datatypes_disable_auto": false, "use_remote_user": null, "message_box_class": "info"}, "welcome_url": "/galaxy/root/welcome"},
                {}
            );
        </script>
    </body>
</html>


Thanks and Regards,
Ashok Varadharajan

___________________________________________________________
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Re: Problem with downloading datasets using wget or curl

Ashok Varadharajan
Dear Team,

Can anyone help us to solve the below issue?

Our galaxy users could not download large sequencing data using wget or curl.

Thanks and Regards,
Ashok Varadharajan

On Wed, Mar 22, 2017 at 10:15 AM, Ashok Varadharajan <[hidden email]> wrote:
Dear Team,

We are running galaxy-16.07 behind the proxy using nginx, uwsgi and supervisor in scientific linux 7. I have problem with downloading datasets using wget. 

I am getting the following html for all my datasets in the galaxy when I try to download it using wget [for example:  wget http://{GALAXYURL}/galaxy/datasets/xxxxxxxxxxxx/display?to_ext=tabular]

Can anyone help me to solve this issue ?


<!DOCTYPE HTML>
<html>
    <!--js-app.mako-->
    <head>
        <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
        <meta name="viewport" content="maximum-scale=1.0">
        <meta http-equiv="X-UA-Compatible" content="IE=Edge,chrome=1">
        <title>Galaxy</title>
        <link rel="index" href="/galaxy/"/>
        <link href="/galaxy/static/style/jquery.rating.css?v=1489572328" media="screen" rel="stylesheet" type="text/css" />
<link href="/galaxy/static/style/jquery-ui/smoothness/jquery-ui.css?v=1489572328" media="screen" rel="stylesheet" type="text/css" />
<link href="/galaxy/static/style/base.css?v=1489572328" media="screen" rel="stylesheet" type="text/css" />
<link href="/galaxy/static/style/bootstrap-tour.css?v=1489572328" media="screen" rel="stylesheet" type="text/css" />
    <script type="text/javascript">
        // this is needed *before* the app code is loaded - many MVC access Galaxy.root for their url
        // TODO: change this by using a common Backbone.Model base class and url fn
        window.Galaxy = { root: '/galaxy/' };
    </script>
    </head>
    <body scroll="no" class="full-content">
        <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;">
            <div id="background"></div>
            <div id="masthead" class="navbar navbar-fixed-top navbar-inverse"></div>
            <div id="messagebox" style="display: none;"></div>
            <div id="inactivebox" class="panel-warning-message" style="display: none;"></div>
        </div><!--end everything-->
        <div id='dd-helper' style="display: none;"></div>
    <noscript>
        <div class="overlay overlay-background noscript-overlay">
            <div>
                <h3 class="title">Javascript Required for Galaxy</h3>
                <div>
                    The Galaxy analysis interface requires a browser with Javascript enabled.<br>
                    Please enable Javascript and refresh this page.
                </div>
            </div>
        </div>
    </noscript>
        <script src="/galaxy/static/scripts/bundled/libs.bundled.js?v=1489572328" type="text/javascript"></script>
<script src="/galaxy/static/scripts/bundled/login.bundled.js?v=1489572328" type="text/javascript"></script>
        <script type="text/javascript">
            app(
                {"redirect": "/galaxy/datasets/xxxxxxxxxxxxxxxx/display", "show_welcome_with_login": false, "user": {"quota_percent": null, "id": null, "total_disk_usage": 0.0, "nice_total_disk_usage": "0 bytes"}, "openid_providers": [], "root": "/galaxy/", "config": {"communication_server_host": "http://localhost", "ftp_upload_site": null, "mailing_lists": "https://wiki.galaxyproject.org/MailingLists", "nginx_upload_path": "/galaxy/api/tools", "terms_url": null, "enable_unique_workflow_defaults": false, "wiki_url": "https://wiki.galaxyproject.org/", "version_major": "16.07", "support_url": "https://wiki.galaxyproject.org/Support", "persistent_communication_rooms": [], "remote_user_logout_href": null,
"message_box_content": null, "logo_src": "/galaxy/static/images/galaxyIcon_noText.png", "biostar_url_redirect": "http://{GALAXY_URL}/galaxy/biostar/biostar_redirect", "message_box_visible": false, "ftp_upload_dir": "{ftp_upload_dir}", "logo_url": "/galaxy/", "brand": "{BRAND}", "search_url": "http://galaxyproject.org/search/usegalaxy/", "screencasts_url": null, "ga_code": null, "require_login": true, "communication_server_port": 7070, "lims_doc_url": "https://usegalaxy.org/u/rkchak/p/sts", "inactivity_box_content": "Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address.", "citation_url": "https://wiki.galaxyproject.org/CitingGalaxy", "allow_user_creation": false, "is_admin_user": false, "allow_user_dataset_purge": true, "server_startttime": 1489572328,
"biostar_url": null, "datatypes_disable_auto": false, "use_remote_user": null, "message_box_class": "info"}, "welcome_url": "/galaxy/root/welcome"},
                {}
            );
        </script>
    </body>
</html>


Thanks and Regards,
Ashok Varadharajan





___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
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